https://wiki.pymol.org/api.php?action=feedcontributions&feedformat=atom&user=Philaltist 2026-07-04T15:48:30Z User contributions MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Resicolor_plugin&diff=8610 2008-07-30T01:53:27Z

<p>Philaltist: </p> <hr /> <div>==Description==<br /> Here is a small plugin to color proteins according to residue type. Save the following text as &quot;resicolor.py&quot; in your somewhere/PyMOL/modules/pmg_tk/startup directory, and it should add itself to the plugin menu at the next pymol startup. This functionality is also available as a script ([[resicolor]]).<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #plugin contributed by Philippe Garteiser garteiserp@omrf.org<br /> from Tkinter import *<br /> from pymol import cmd<br /> import tkSimpleDialog<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor',<br /> command = lambda s=self : getselection(s))<br /> <br /> def resicolor(selection):<br /> if selection: # None is returned for user cancel<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word)<br /> <br /> def getselection(app):<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> resicolor(selection)<br /> <br /> &lt;/source&gt;<br /> <br /> [[Category:Plugins]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor_plugin&diff=8609 2007-04-21T18:53:31Z

<p>Philaltist: </p> <hr /> <div>==Description==<br /> Here is a small plugin to color proteins according to residue type. Save the following text as &quot;resicolor.py&quot; in your somewhere/PyMOL/modules/pmg_tk/startup directory, and it should add itself to the plugin menu at the next pymol startup. This functionality is also available as a script ([[resicolor]]).<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu<br /> from Tkinter import *<br /> from pymol import cmd<br /> import tkSimpleDialog<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor',<br /> command = lambda s=self : getselection(s))<br /> <br /> def resicolor(selection):<br /> if selection: # None is returned for user cancel<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word)<br /> <br /> def getselection(app):<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> resicolor(selection)<br /> <br /> &lt;/source&gt;<br /> <br /> [[Category:Plugins]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9462 2007-04-21T18:41:11Z

<p>Philaltist: </p> <hr /> <div>==Description==<br /> <br /> Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A.<br /> This functionality is also available as a plugin ([[Resicolor_plugin]]).<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor_plugin&diff=8608 2007-04-21T18:39:26Z

<p>Philaltist: </p> <hr /> <div>==Description==<br /> Here is a small plugin to color proteins according to residue type. Save the following text as &quot;resicolor.py&quot; in your somewhere/PyMOL/modules/pmg_tk/startup directory, and it should add itself to the plugin menu at the next pymol startup. This functionality is also available as a script ([[resicolor]]).<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu<br /> from Tkinter import *<br /> from pymol import cmd<br /> import tkSimpleDialog<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor2',<br /> command = lambda s=self : getselection(s))<br /> <br /> def resicolor(selection):<br /> if selection: # None is returned for user cancel<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word)<br /> <br /> def getselection(app):<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> resicolor(selection)<br /> <br /> &lt;/source&gt;<br /> <br /> [[Category:Plugins]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9461 2007-04-21T18:37:54Z

<p>Philaltist: </p> <hr /> <div>Hello !<br /> <br /> Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A.<br /> This functionality is also available as a [http://pymolwiki.org/index.php/Resicolor_plugin plugin].<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor_plugin&diff=8607 2007-04-21T18:36:08Z

<p>Philaltist: New page: ==Description== Here is a small plugin to color proteins according to residue type. Save the following text as &quot;resicolor.py&quot; in your somewhere/PyMOL/modules/pmg_tk/startup directory, and ...</p> <hr /> <div>==Description==<br /> Here is a small plugin to color proteins according to residue type. Save the following text as &quot;resicolor.py&quot; in your somewhere/PyMOL/modules/pmg_tk/startup directory, and it should add itself to the plugin menu at the next pymol startup. This functionality is also available as a script.<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu<br /> from Tkinter import *<br /> from pymol import cmd<br /> import tkSimpleDialog<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor2',<br /> command = lambda s=self : getselection(s))<br /> <br /> def resicolor(selection):<br /> if selection: # None is returned for user cancel<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word)<br /> <br /> def getselection(app):<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> resicolor(selection)<br /> <br /> &lt;/source&gt;<br /> <br /> [[Category:Plugins]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9460 2007-04-21T18:27:17Z

<p>Philaltist: </p> <hr /> <div>Hello !<br /> <br /> Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A.<br /> This functionality is also available as a plugin.<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9459 2007-04-10T20:25:05Z

<p>Philaltist: </p> <hr /> <div>Hello !<br /> <br /> Here is a small plugin to color proteins according to residue type. Copy this into a file saved as resicolor.py inside your plugins startup directory, and it should add itself to the plugins menu at the next pymol startup. The script version (accessible from command line) is presented below.<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu<br /> from Tkinter import *<br /> from pymol import cmd<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor',<br /> command = lambda s=self : resicolor(s))<br /> class resicolor:<br /> def __init__(self,app):<br /> import tkSimpleDialog<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> if selection: # None is returned for user cancel<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> &lt;/source&gt;<br /> <br /> Here is the corresponding script file. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A. <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9458 2007-04-10T19:01:43Z

<p>Philaltist: </p> <hr /> <div>Hello !<br /> <br /> Here is a small plugin to color proteins according to residue type. Copy this into a file saved as resicolor.py inside your plugins startup directory, and it should add itself to the plugins menu at the next pymol startup. The script version (accessible from command line) is presented below.<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu<br /> from Tkinter import *<br /> from pymol import cmd<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor',<br /> command = lambda s=self : resicolor(s))<br /> class resicolor:<br /> def __init__(self,app):<br /> import tkSimpleDialog<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> if selection: # None is returned for user cancel<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.do ('getchem')<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> &lt;/source&gt;<br /> <br /> Here is the corresponding script file. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A. <br /> &lt;source lang=&quot;python&quot;&gt;<br /> #script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.do ('getchem')<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9457 2007-04-10T18:49:27Z

<p>Philaltist: </p> <hr /> <div>Hello !<br /> <br /> Here is a small plugin to color proteins according to residue type. Copy this into a file saved as resicolor.py inside your plugins startup directory, and it should add itself to the plugins menu at the next pymol startup. The script version (accessible from command line) is presented below.<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from Tkinter import *<br /> from pymol import cmd<br /> <br /> def __init__(self):<br /> # Simply add the menu entry and callback<br /> self.menuBar.addmenuitem('Plugin', 'command',<br /> 'resicolor',<br /> label = 'resicolor',<br /> command = lambda s=self : resicolor(s))<br /> class resicolor:<br /> def __init__(self,app):<br /> import tkSimpleDialog<br /> selection=tkSimpleDialog.askstring('resicolor',<br /> 'Please enter a selection',<br /> parent=app.root)<br /> if selection:<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none') <br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.do ('getchem')<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> &lt;/source&gt;<br /> <br /> Here is the corresponding script file. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A. <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.do ('getchem')<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9456 2007-04-10T15:16:18Z

<p>Philaltist: </p> <hr /> <div>Hello !<br /> <br /> Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A. <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.do ('getchem')<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)<br /> &lt;/source&gt;<br /> <br /> [[Category:Script_Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Resicolor&diff=9455 2007-04-10T15:15:03Z

<p>Philaltist: New page: Hello ! Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the s...</p> <hr /> <div>Hello !<br /> <br /> Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: &quot;run resicolor.py&quot;. Then, issuing &quot;resicolor&quot; will apply the scheme. Selections are supported: &quot;resicolor chain A&quot; will apply the scheme only to chain A. <br /> <br /> from pymol import cmd<br /> <br /> def resicolor(selection='all'):<br /> <br /> '''USAGE: resicolor &lt;selection&gt;<br /> colors all or the given selection with arbitrary<br /> coloring scheme.<br /> '''<br /> cmd.select ('calcium','resn ca or resn cal')<br /> cmd.select ('acid','resn asp or resn glu or resn cgu')<br /> cmd.select ('basic','resn arg or resn lys or resn his')<br /> cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')<br /> cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')<br /> cmd.select ('cys','resn cys or resn cyx')<br /> cmd.select ('backbone','name ca or name n or name c or name o')<br /> cmd.select ('none')<br /> <br /> print selection<br /> code={'acid' : 'red' ,<br /> 'basic' : 'blue' ,<br /> 'nonpolar': 'orange' ,<br /> 'polar' : 'green' ,<br /> 'cys' : 'yellow'}<br /> cmd.do ('getchem')<br /> cmd.select ('none')<br /> for elem in code:<br /> line='color '+code[elem]+','+elem+'&amp;'+selection<br /> print line<br /> cmd.do (line)<br /> word='color white,backbone &amp;'+selection<br /> print word<br /> cmd.do (word) #Used to be in code, but looks like<br /> #dictionnaries are accessed at random<br /> cmd.hide ('everything','resn HOH')<br /> <br /> cmd.extend ('resicolor',resicolor)</div>

Philaltist https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3885 2007-04-10T15:10:56Z

<p>Philaltist: </p> <hr /> <div>* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.<br /> <br /> * [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.<br /> <br /> * [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.<br /> <br /> * [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).<br /> <br /> * [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)<br /> <br /> * [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> * [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.<br /> <br /> * [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X<br /> <br /> * [[Show aromatics]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for aromatic residues displayed as green &quot;sticks&quot;. Usage: Save this as &quot;show_aromatics.pml&quot;, load your protein in PyMOL, and run the script (select &quot;Run&quot; from the &quot;File&quot; menu). (PyMOL script; TStout)<br /> <br /> * [[Show hydrophobics]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for hydrophobic residues displayed as orange &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show charged]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show hydrophilic]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for hydrophilic residues displayed as green &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as &quot;NMRcnstr.py&quot; load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display. <br /> <br /> * [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])<br /> <br /> * [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.<br /> <br /> * [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.<br /> <br /> * [[CGO Text]] -- Creates a 3D-CGO text object.<br /> <br /> * [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).<br /> <br /> * [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).<br /> <br /> * [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').<br /> <br /> * [[Split Movement]] -- Moves two parts of one object into different directions.<br /> <br /> * [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.<br /> <br /> * [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.<br /> <br /> * [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).<br /> <br /> * [[grepset]] -- List all settings matching a given keyword. - ''by EHP''<br /> <br /> * [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''<br /> <br /> * [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''<br /> <br /> * [[Measure Distance]] -- Measures the distance between two atoms (Python script).<br /> <br /> * [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.<br /> <br /> * [[Color Objects]] -- Colors all objects differently (Python script).<br /> <br /> * [[Key Wait]] -- Process key events in a Python script.<br /> <br /> * [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)<br /> <br /> * [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)<br /> <br /> * [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)<br /> <br /> * [[resicolor]] -- Colors proteins according to residue type.<br /> <br /> * [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.<br /> <br /> * [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!<br /> <br /> * [[grepsel]] -- Make named selections using regular expressions (protein sequence).<br /> <br /> * [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.<br /> <br /> * [[Plane Wizard]] -- Wizard to draw planes between three picked points.<br /> <br /> * [[Slerpy]] -- Pymol command extensions for key frame animation movie making.<br /> <br /> * [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence<br /> <br /> [[Category:Scripting|Script Library]]</div>

Philaltist https://wiki.pymol.org/index.php?title=User_talk:Philaltist&diff=10761 2006-06-02T18:02:37Z

<p>Philaltist: </p> <hr /> <div>Do you think that a singe page for all the cartoon_helix types would be better than separate pages? e.g. putting the fance, normal, and cylindrical all on one page --Adam Shea<br /> <br /> Yes I think it would be best to have all the cartoon_helix links of the settings page point to the same page. Do you know how to do that ? I think it would be less hairy/redundant than a 'related settings' section in multiple pages. --Philippe Garteiser</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_cylindrical_helices&diff=4965 2006-06-02T15:10:54Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This is a display setting. It replaces cartoon-represented helices by cylinders.<br /> <br /> ==Syntax==<br /> <br /> set cartoon_cylindrical_helices, 1 to turn on<br /> <br /> set cartoon_cylindrical_helices, 0 to turn off<br /> <br /> ==Result==<br /> [[image:Notcylindre.JPG|frame|Default representation|left]]<br /> [[image:Cylindre.JPG|frame|Cylindre helix|center]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_cylindrical_helices&diff=4964 2006-06-02T15:10:41Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This is a display setting. It replaces cartoon-represented helices by cylinders.<br /> <br /> ==Syntax==<br /> <br /> set cartoon_cylindrical_helices, 1 to turn on<br /> <br /> set cartoon_cylindrical_helices, 0 to turn off<br /> <br /> ==Result==<br /> [[image:Notcylindre.JPG|frame|Default representation|left]]<br /> [[image:Cylindre.JPG|frame|Cylindre helices|center]]</div>

Philaltist https://wiki.pymol.org/index.php?title=File:Cylindre.JPG&diff=1495 2006-06-02T15:09:14Z

<p>Philaltist: </p> <hr /> <div></div>

Philaltist https://wiki.pymol.org/index.php?title=File:Notcylindre.JPG&diff=2181 2006-06-02T15:08:45Z

<p>Philaltist: </p> <hr /> <div></div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_cylindrical_helices&diff=4963 2006-06-02T15:08:26Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This is a display setting. It replaces cartoon-represented helices by cylinders.<br /> <br /> ==Syntax==<br /> <br /> set cartoon_cylindrical_helices, 1 to turn on<br /> <br /> set cartoon_cylindrical_helices, 0 to turn off<br /> <br /> ==Result==</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10081 2006-06-02T15:05:47Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode [[sphere_color]] <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Sphere_color&diff=5536 2006-06-01T21:20:23Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> set sphere_color allows to color spheres independently from the rest of the representations. <br /> <br /> ==Syntax==<br /> PyMOL&gt;set sphere_color,''color''<br /> <br /> where ''color'' can be :<br /> <br /> -any usual colors (blue, yellow, grey50,...)<br /> <br /> -number-coded colors (1:black, 2:blue, 3:greenish, ...)<br /> <br /> -special code -1 to revert to original chameleon setting (''set sphere_color,-1'')<br /> <br /> ==Related settings==<br /> <br /> [[cartoon_color]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_color&diff=938 2006-06-01T21:18:55Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> set cartoon_color allows to color cartoons independently from the rest of the representations. <br /> <br /> ==Syntax==<br /> PyMOL&gt;set cartoon_color,''color''<br /> <br /> where ''color'' can be :<br /> <br /> -any usual colors (blue, yellow, grey50,...)<br /> <br /> -number-coded colors (1:black, 2:blue, 3:greenish, ...)<br /> <br /> -special code -1 to revert to original chameleon setting (''set cartoon_color,-1'')<br /> <br /> ==Related settings==<br /> <br /> [[sphere_color]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10080 2006-06-01T21:16:28Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode [[sphere_color]] <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_color&diff=937 2006-06-01T21:14:07Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> set cartoon_color allows to color cartoons independently from the rest of the representations. <br /> <br /> ==Syntax==<br /> PyMOL&gt;set cartoon_color,''color''<br /> <br /> where ''color'' can be :<br /> <br /> -any usual colors (blue, yellow, grey50,...)<br /> <br /> -number-coded colors (1:black, 2:blue, 3:greenish, ...)<br /> <br /> -special code -1 to revert to original chameleon setting (''set cartoon_color,-1'')<br /> <br /> ==Related settings==<br /> <br /> [[set sphere_color]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Seq_view_location&diff=9771 2006-06-01T18:24:36Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> seq_view_location affects the location of the sequence viewer.<br /> <br /> ==Syntax==<br /> <br /> set seq_view_location, ''integer''<br /> <br /> set ''integer'' to 0 to get the default (the viewer is on top of the internal window)<br /> <br /> set ''integer'' to 1 or higher to locate the sequence viewer just above the command line.<br /> <br /> <br /> ==Related settings==<br /> [[seq_view]]<br /> <br /> [[seq_view_color]]<br /> <br /> [[seq_view_discrete_by_state]]<br /> <br /> [[seq_view_fill_char]]<br /> <br /> [[seq_view_fill_color]]<br /> <br /> [[seq_view_format]]<br /> <br /> [[seq_view_label_color]]<br /> <br /> [[seq_view_label_mode]]<br /> <br /> [[seq_view_label_spacing]]<br /> <br /> [[seq_view_label_start]]<br /> <br /> [[seq_view_overlay]]<br /> <br /> [[seq_view_unaligned_color]]<br /> <br /> [[seq_view_unaligned_mode]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Seq_view_location&diff=9770 2006-06-01T18:24:03Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> seq_view_locations affects the location of the sequence viewer.<br /> <br /> ==Syntax==<br /> <br /> set seq_view, ''integer''<br /> <br /> set ''integer'' to 0 to get the default (the viewer is on top of the internal window)<br /> <br /> set ''integer'' to 1 or higher to locate the sequence viewer just above the command line.<br /> <br /> <br /> ==Related settings==<br /> [[seq_view]]<br /> <br /> [[seq_view_color]]<br /> <br /> [[seq_view_discrete_by_state]]<br /> <br /> [[seq_view_fill_char]]<br /> <br /> [[seq_view_fill_color]]<br /> <br /> [[seq_view_format]]<br /> <br /> [[seq_view_label_color]]<br /> <br /> [[seq_view_label_mode]]<br /> <br /> [[seq_view_label_spacing]]<br /> <br /> [[seq_view_label_start]]<br /> <br /> [[seq_view_overlay]]<br /> <br /> [[seq_view_unaligned_color]]<br /> <br /> [[seq_view_unaligned_mode]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10079 2006-06-01T18:19:57Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Talk:Settings&diff=130 2006-06-01T16:54:56Z

<p>Philaltist: </p> <hr /> <div>awesome idea, Shea !</div>

Philaltist https://wiki.pymol.org/index.php?title=Sphere_scale&diff=10329 2006-06-01T16:02:57Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This setting affects the apparent radius of spheres in the sphere representation. Default scale is set to 1.0.<br /> <br /> ==Syntax==<br /> <br /> set sphere_scale, ''size''<br /> <br /> ''size'' can be any float number. Using 0.25 gives a nice balls&amp;sticks representation with both lines and spheres turned on.<br /> <br /> set sphere_scale by itself will revert to default.<br /> <br /> ==Related settings==<br /> [[sphere_color]]<br /> <br /> [[sphere_mode]]<br /> <br /> [[sphere_point_max_size]]<br /> <br /> [[sphere_point_size]]<br /> <br /> [[sphere_quality]]<br /> <br /> [[sphere_solvent]]<br /> <br /> [[sphere_transparency]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Sphere_scale&diff=10328 2006-06-01T16:02:42Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This setting affects the apparent radius of spheres in the sphere representation. Default scale is set to 1.0.<br /> <br /> ==Syntax==<br /> <br /> set sphere_scale, ''size''<br /> <br /> ''size'' can be any float number. Using 0.25 gives a nice balls&amp;sticks representation with both lines and spheres turned on.<br /> <br /> set sphere_scale by itself will revert to default.<br /> <br /> ==Related settings==<br /> [[sphere_color]]<br /> [[sphere_mode]]<br /> [[sphere_point_max_size]]<br /> [[sphere_point_size]]<br /> [[sphere_quality]]<br /> [[sphere_solvent]]<br /> [[sphere_transparency]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Sphere_scale&diff=10327 2006-06-01T15:59:51Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This setting affects the apparent radius of spheres in the sphere representation. Default scale is set to 1.0.<br /> <br /> ==Syntax==<br /> <br /> set sphere_scale, ''size''<br /> <br /> ''size'' can be any float number. Using 0.25 gives a nice balls&amp;sticks representation with both lines and spheres turned on.<br /> <br /> set sphere_scale by itself will revert to default.<br /> <br /> ==Related settings==</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10078 2006-06-01T15:55:59Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Seq_view&diff=9745 2006-06-01T15:52:52Z

<p>Philaltist: /* Related settings */</p> <hr /> <div>==Overview==<br /> <br /> seq_view turns the sequence viewer on and off. The sequence viewer is a very handy tool, you can use it for example to select residues very easily.<br /> <br /> ==Syntax==<br /> <br /> set seq_view, 1 to turn the sequence viewer on.<br /> <br /> set seq_view, 0 to turn the sequence viewer off.<br /> <br /> <br /> ==Related settings==<br /> [[seq_view_color]]<br /> <br /> [[seq_view_discrete_by_state]]<br /> <br /> [[seq_view_fill_char]]<br /> <br /> [[seq_view_fill_color]]<br /> <br /> [[seq_view_format]]<br /> <br /> [[seq_view_label_color]]<br /> <br /> [[seq_view_label_mode]]<br /> <br /> [[seq_view_label_spacing]]<br /> <br /> [[seq_view_label_start]]<br /> <br /> [[seq_view_location]]<br /> <br /> [[seq_view_overlay]]<br /> <br /> [[seq_view_unaligned_color]]<br /> <br /> [[seq_view_unaligned_mode]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Seq_view&diff=9744 2006-06-01T15:52:31Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> seq_view turns the sequence viewer on and off. The sequence viewer is a very handy tool, you can use it for example to select residues very easily.<br /> <br /> ==Syntax==<br /> <br /> set seq_view, 1 to turn the sequence viewer on.<br /> <br /> set seq_view, 0 to turn the sequence viewer off.<br /> <br /> <br /> ==Related settings==<br /> [[seq_view_color]]<br /> [[seq_view_discrete_by_state]]<br /> [[seq_view_fill_char]]<br /> [[seq_view_fill_color]]<br /> [[seq_view_format]]<br /> [[seq_view_label_color]]<br /> [[seq_view_label_mode]]<br /> [[seq_view_label_spacing]]<br /> [[seq_view_label_start]]<br /> [[seq_view_location]]<br /> [[seq_view_overlay]]<br /> [[seq_view_unaligned_color]]<br /> [[seq_view_unaligned_mode]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Seq_view&diff=9743 2006-06-01T15:43:28Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> seq_view turns the sequence viewer on and off. The sequence viewer is a very handy tool, you can use it for example to select residues very easily.<br /> <br /> ==Syntax==<br /> <br /> set seq_view, 1 to turn the sequence viewer on.<br /> <br /> set seq_view, 0 to turn the sequence viewer off.<br /> <br /> <br /> ==Related settings==</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10077 2006-06-01T15:40:37Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10074 2006-05-31T20:01:51Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> parser: matching setting:<br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> cartoon_color ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> cartoon_fancy_helices ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> cartoon_smooth_loops scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> internal_gui slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output<br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Internal_prompt&diff=8360 2006-05-31T20:01:26Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> Look even nerdier in front of your friends ! set internal_prompt,f ! <br /> <br /> internal_prompt turns the internal 'PyMOL&gt;' prompt on or off. The typed commands are not seen anymore, unless you use the esc toggle, which allows you as usual to see the console dialogue. The last line of verbose is still visible where the command line used to be. <br /> <br /> ==Syntax==<br /> <br /> set internal_prompt,''boolean''<br /> <br /> where ''boolean'' can be either of true, false, t, f, 1 or 0.<br /> <br /> ==Feature request==<br /> I wish it was possible to replace the usual prompt by any given string, and especially by the current path like it is possible in other consoles.</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10073 2006-05-31T19:52:10Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 5 done, 495 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> parser: matching setting:<br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> cartoon_color ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> cartoon_fancy_helices ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> cartoon_smooth_loops scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> internal_gui slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output<br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_smooth_loops&diff=5005 2006-05-31T19:20:00Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> This is a display setting. When set to off, the cartoon will follow a path that is splined between each alpha carbons. This sometimes yields representations that are pretty frizzy. Turning this setting on will make the cartoon follow a smoother (but less conservative) path so that the representation is easier on the eyes. Use with caution, since false conclusions can be drawn by solely examining a smoothed cartoon trace. It is always best (for non-representation purposes) to also have a line trace so that the backbone is precisely located.<br /> [[Image:Frizz.JPG|frame|set cartoon_smooth_loops,0 : the cartoon passes through each alpha-carbon|left]]<br /> [[Image:Smooth.JPG|frame|set cartoon_smooth_loops,1 : the cartoon is straighter but less conservative|center]]<br /> ==Syntax==<br /> turn on:<br /> set cartoon_smooth_loops, 1<br /> turn off:<br /> set cartoon_smooth_loops, 0<br /> <br /> ===Additional remarks===<br /> I do not know precisely how the smoothed trace is generated, probably by some splining mode. Could someone more knowledgeable than me edit to be more precise ?</div>

Philaltist https://wiki.pymol.org/index.php?title=File:Smooth.JPG&diff=2563 2006-05-31T19:15:56Z

<p>Philaltist: </p> <hr /> <div></div>

Philaltist https://wiki.pymol.org/index.php?title=File:Frizz.JPG&diff=2070 2006-05-31T19:15:46Z

<p>Philaltist: </p> <hr /> <div></div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10072 2006-05-31T19:09:42Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 5 done, 495 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> parser: matching setting:<br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> cartoon_color ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> cartoon_fancy_helices ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> cartoon_smooth_loops scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> internal_gui slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output<br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Bg_rgb&diff=4251 2006-05-31T19:09:15Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> This setting is used to set the color of the background. Any color of the spectrum can be rendered. White backgrounds are often desirable for publication images.<br /> <br /> ==Syntax==<br /> <br /> set bg_rgb,[''float1'',''float2'',''float3'']<br /> <br /> each float must be between 0.0 and 1.0<br /> <br /> float1: red component<br /> <br /> float2: green component<br /> <br /> float3: blue component<br /> <br /> <br /> <br /> example: set bg_rgb,[1,1,1]<br /> <br /> will color the background in white.</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10071 2006-05-31T19:02:06Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 4 done, 496 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> parser: matching setting:<br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> cartoon_color ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> cartoon_fancy_helices ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> cartoon_smooth_loops scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> internal_gui slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output<br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10070 2006-05-31T18:56:29Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 4 done, 496 to go !<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> parser: matching setting:<br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> cartoon_color ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> cartoon_fancy_helices ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> cartoon_smooth_loops scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> internal_gui slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output<br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_color&diff=936 2006-05-31T18:54:43Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> <br /> set cartoon_color allows to color cartoons independently from the rest of the representations. <br /> <br /> ==Syntax==<br /> PyMOL&gt;set cartoon_color,''color''<br /> <br /> where ''color'' can be :<br /> <br /> -any usual colors (blue, yellow, grey50,...)<br /> <br /> -number-coded colors (1:black, 2:blue, 3:greenish, ...)<br /> <br /> -special code -1 to revert to original chameleon setting (''set cartoon_color,-1'')</div>

Philaltist https://wiki.pymol.org/index.php?title=Settings&diff=10069 2006-05-31T18:45:36Z

<p>Philaltist: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. There's over 500.<br /> <br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> [[cartoon_fancy_helices]] ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> parser: matching setting:<br /> active_selections ray_default_renderer <br /> all_states ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> antialias ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss ray_opaque_background <br /> auto_hide_selections ray_orthoscopic <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens ray_shadow <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections ray_shadows <br /> auto_show_spheres ray_texture <br /> auto_zoom ray_texture_settings <br /> backface_cull ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> bg_rgb ray_trace_fog <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode ray_trace_frames <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> cartoon_color ray_transparency_shadows <br /> cartoon_cylindrical_helices ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> cartoon_discrete_colors ray_triangle_fudge <br /> cartoon_dumbbell_length reflect <br /> cartoon_dumbbell_radius reflect_power <br /> cartoon_dumbbell_width retain_order <br /> cartoon_fancy_helices ribbon_color <br /> cartoon_fancy_sheets ribbon_nucleic_acid_mode <br /> cartoon_flat_cycles ribbon_power <br /> cartoon_flat_sheets ribbon_power_b <br /> cartoon_helix_radius ribbon_radius <br /> cartoon_highlight_color ribbon_sampling <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality ribbon_width <br /> cartoon_loop_radius robust_logs <br /> cartoon_nucleic_acid_color rock_delay <br /> cartoon_nucleic_acid_mode roving_byres <br /> cartoon_oval_length roving_cartoon <br /> cartoon_oval_quality roving_delay <br /> cartoon_oval_width roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> cartoon_rect_length roving_map3_level <br /> cartoon_rect_width roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> cartoon_ring_mode roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> cartoon_ring_transparency roving_ribbon <br /> cartoon_ring_width roving_selection <br /> cartoon_round_helices roving_spheres <br /> cartoon_sampling roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> cartoon_smooth_loops scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> cartoon_transparency sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> dash_gap sculpt_plan_weight <br /> dash_length sculpt_pyra_weight <br /> dash_radius sculpt_tors_tolerance <br /> dash_round_ends sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter <br /> dot_width selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin selection_width <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path seq_view <br /> field_of_view seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor seq_view_location <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> half_bonds simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> internal_gui slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> internal_prompt spec_direct <br /> isomesh_auto_state spec_direct_power <br /> label_color spec_power <br /> label_font_id spec_reflect <br /> label_outline_color specular <br /> label_position specular_intensity <br /> label_shadow_mode sphere_color <br /> label_size sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 sphere_scale <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> line_smooth ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent stick_ball <br /> mesh_type stick_ball_ratio <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit stick_nub <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay stick_transparency <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> orthoscopic surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> pickable sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit transparency <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green two_sided_lighting <br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor valence <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output<br /> <br /> [[Category:Settings|All Settings]]</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_Helix_Settings&diff=6531 2006-05-31T18:36:44Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> This is a display setting.<br /> <br /> It acts on the section of cartoon-represented helices. When turned off, the section is an ellipsoid. When turned on, the section is a line with circles on each end. The resulting helices are pretty slick ribbons with tubular edges &amp;agrave la MolScript.<br /> <br /> ==Syntax==<br /> Turn on:<br /> set cartoon_fancy_helices, 1<br /> <br /> Turn off:<br /> set cartoon_fancy_helices, 0<br /> <br /> ==Result==<br /> [[image:Fancy.JPG|frame|fancy helices|left]]<br /> [[image:default.JPG|frame|default representation|center]]<br /> <br /> ==edit request==<br /> I can't have the &amp;agrave character display properly.</div>

Philaltist https://wiki.pymol.org/index.php?title=Cartoon_Helix_Settings&diff=6530 2006-05-31T18:29:43Z

<p>Philaltist: </p> <hr /> <div>==Overview==<br /> This is a display setting.<br /> <br /> It acts on the section of cartoon-represented helices. When turned off, the section is an ellipsoid. When turned on, the section is a line with circles on each end. The resulting helices are pretty slick ribbons with tubular edges a la MolScript.<br /> <br /> ==Syntax==<br /> Turn on:<br /> set cartoon_fancy_helices, 1<br /> <br /> Turn off:<br /> set cartoon_fancy_helices, 0<br /> <br /> ==Result==<br /> [[image:Fancy.JPG|frame|fancy helices|left]]<br /> [[image:default.JPG|frame|default representation|center]]</div>

Philaltist