PyMOL Wiki - User contributions [en]

Distance

2005-02-22T12:49:51Z

Cmoad:

===DESCRIPTION===
"distance" creates a new distance object between two
selections. It will display all distances within the cutoff.

===USAGE===
distance
distance (selection1), (selection2)
distance name = (selection1), (selection1) [,cutoff [,mode] ]

name = name of distance object
selection1, selection2 = atom selections
cutoff = maximum distance to display
mode = 0 (default)

===PYMOL API===
cmd.distance( string name, string selection1, string selection2,
string cutoff, string mode )
# returns the average distance between all atoms/frames

===NOTES===
The distance wizard makes measuring distances easier than using
the "dist" command for real-time operations.

"dist" alone will show distances between selections (pk1) and (pk1),
which can be set using the PkAt mouse action (usually CTRL-middle-click).

[[Category:Commands|distance]]

Edit Keys

2005-02-22T12:48:24Z

Cmoad:

===EDITING KEYS ===
These are defaults, which can be redefined. Note that while
entering text on the command line, some of these control keys take on
text editing functions instead (CTRL - A, E, and K, and DELETE), so
you should clear the command line before trying to edit atoms.

====ATOM REPLACEMENT====
CTRL-C Replace picked atom with carbon (C)
CTRL-N Replace picked atom with nitrogen (N)
CTRL-O Replace picked atom with oxygen (O)
CTRL-S Replace picked atom with sulpher (S)
CTRL-G Replace picked atom with hydrogen (H)
CTRL-F Replace picked atom with fluorene (F)
CTRL-L Replace picked atom with chlorine (Cl)
CTRL-B Replace picked atom with bromine (Br)
CTRL-I Replace picked atom with iodine (I)

====ATOM MODIFICATION====
CTRL-J Set charge on picked atom to -1
CTRL-K Set charge on picked atom to +1
CTRL-D Remove atom or bond (DELETE works too).
CTRL-Y Add a hydrogen to the current atom
CTRL-R Adjust hydrogens on atom/bond to match valence.
CTRL-E Inverts the picked stereo center, but you must first
indicate the constant portions with the (lb) and (rb)
selections.

CTRL-T Connect atoms in the (lb) and (rb) selections.
CTRL-W Cycle the bond valence on the picked bond.

UNDO and REDO of conformational changes (not atom changes!)

CTRL-Z undo the previous conformational change.
(you can not currently undo atom modifications).
CTRL-A redo the previous conformational change.

[[Category:Commands|edit_keys]]

Deselect

2005-02-22T12:47:01Z

Cmoad:

===DESCRIPTION===
"deselect" disables any and all visible selections

===USAGE===
deselect

===PYMOL API===
cmd.deselect()

[[Category:Commands|deselect]]

Deprotect

2005-02-22T12:46:18Z

Cmoad:

===DESCRIPTION===
"deprotect" reveres the effect of the "protect" command.

===USAGE===
deprotect (selection)

===PYMOL API===
cmd.deprotect(string selection="(all)")

===SEE ALSO===
[[Cmd protect|protect]], [[Cmd mask|mask]], [[Cmd unmask|unmask]], [[Cmd mouse|mouse]], [[Cmd editing|editing]]

[[Category:Commands|deprotect]]

Deprotect

2005-02-22T12:46:02Z

Cmoad:

Deprotect

2005-02-22T12:45:21Z

Cmoad:

===DESCRIPTION===
"deprotect" reveres the effect of the "protect" command.

===USAGE===
deprotect (selection)

===PYMOL API===
<source lang="python">
cmd.deprotect(string selection="(all)")
</source>

===SEE ALSO===
[[Cmd protect|protect]], [[Cmd mask|mask]], [[Cmd unmask|unmask]], [[Cmd mouse|mouse]], [[Cmd editing|editing]]

[[Category:Commands|deprotect]]

Deprotect

2005-02-22T12:42:43Z

Cmoad:

===DESCRIPTION===
"deprotect" reveres the effect of the "protect" command.

===USAGE===
deprotect (selection)

===PYMOL API===
<source lang="python">
cmd.deprotect(string selection="(all)")
</source>

===SEE ALSO===
[[Cmd protect]], [[Cmd mask]], [[Cmd unmask]], [[Cmd mouse]], [[Cmd editing]]

[[Category:Commands|deprotect]]

Deprotect

2005-02-22T12:42:21Z

Cmoad:

===DESCRIPTION===
"deprotect" reveres the effect of the "protect" command.

===USAGE===
deprotect (selection)

===PYMOL API===
<source lang="python">
cmd.deprotect(string selection="(all)")
</source>

===SEE ALSO===

[[Cmd protect]], [[Cmd mask]], [[Cmd unmask]], [[Cmd mouse]], [[Cmd editing]]

[[Category:Commands|deprotect]]

Align

2005-02-18T18:35:05Z

Cmoad:

===DESCRIPTION===
"align" performs a sequence alignment followed by a structural
alignment, and then carrys out zero or more cycles of refinement
in order to reject structural outliers found during the fit.

===USAGE===
<source lang="python">
align (source), (target) [,cutoff [,cycles [,gap [,extend \
[,skip [,object [,matrix [, quiet ]]]]]]]]
</source>

===PYMOL API===
<source lang="python">
cmd.align( string source, string target, float cutoff=2.0,
int cycles=2, float gap=-10.0, float extend=-0.5,
float extend=-0.5,int skip=0, string object=None,
string matrix="BLOSUM62",int quiet=1 )
</source>

===NOTE===
If object is not None, then align will create an object which
indicates which atoms were paired between the two structures

===EXAMPLES===
<source lang="python">
align prot1////CA, prot2, object=alignment
</source>

===SEE ALSO===
[[Cmd fit|fit]], [[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]]

[[Category:Commands|align]]

Main Page

2005-02-17T21:45:34Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* A wiki edit/user policy is needed.
* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:Discussion|Discussion]]
## [[:Category:PyMOL Beta|The Bleeding Edge]]
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Using the GUI]]
## [[Launching PyMOL]]
### [[Command Line Options]]
### [[Launching From a Script]]
## [[Mouse Controls]]
## [[Objects and Selections]]
### [[Working with Objects]]
### [[Working with Selections]]
### [[Selector Quick Reference]]
#### [[Single-word Selectors]]
#### [[Property Selectors]]
#### [[Selection Algebra]]
#### [[Selection Macros]]
### [[Representations]]
#### [[Lines]]
#### [[Sticks]]
#### [[Cartoon]]
#### [[Surface]]
#### [[Mesh]]
#### [[Spheres]]
#### [[Dots]]
### [[Color]]
### [[Displaying biochemical properties]]
## [[Display Settings]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
## [[Scenes]]
## [[Mouse Settings]]
## [[Wizards]]
## [[Plugins]]
## [[Ray-tracing]]
## [[Settings Reference (all settings and what they do)]]
## [[Movies and Animations]]
## [[Structure Alignment]]
## [[Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[PyMOL Command Script]]
## [[PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Example Scripts]]
## [[Script Library]]
# [[:Category:Plugins|Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T21:44:35Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* A wiki edit/user policy is needed.
* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:Discussion|Discussion]]
## [[:Category:PyMOL Beta|The Bleeding Edge]]
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Using the GUI]]
## [[Launching PyMOL]]
### [[Command Line Options]]
### [[Launching From a Script]]
## [[Mouse Controls]]
## [[Objects and Selections]]
### [[Working with Objects]]
### [[Working with Selections]]
### [[Selector Quick Reference]]
#### [[Single-word Selectors]]
#### [[Property Selectors]]
#### [[Selection Algebra]]
#### [[Selection Macros]]
### [[Representations]]
#### [[Lines]]
#### [[Sticks]]
#### [[Cartoon]]
#### [[Surface]]
#### [[Mesh]]
#### [[Spheres]]
#### [[Dots]]
### [[Color]]
### [[Displaying biochemical properties]]
## [[Display Settings]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
## [[Scenes]]
## [[Mouse Settings]]
## [[Wizards]]
## [[Plugins]]
## [[Ray-tracing]]
## [[Settings Reference (all settings and what they do)]]
## [[Movies and Animations]]
## [[Structure Alignment]]
## [[Structure Alignment Editor]]
# [[:Category:Commands|Command Language]] (I added a sample category. Should we continue with something like this?) [[User:Cmoad|Charlie]]
## [[PyMOL Command Script]]
## [[PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Example Scripts]]
## [[Script Library]]
# [[:Category:Plugins|Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-02-17T21:44:08Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* A wiki edit/user policy is needed.
* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:Discussion|Discussion]]
## [[:Category:PyMOL Beta|The Bleeding Edge]]
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Using the GUI]]
## [[Launching PyMOL]]
### [[Command Line Options]]
### [[Launching From a Script]]
## [[Mouse Controls]]
## [[Objects and Selections]]
### [[Working with Objects]]
### [[Working with Selections]]
### [[Selector Quick Reference]]
#### [[Single-word Selectors]]
#### [[Property Selectors]]
#### [[Selection Algebra]]
#### [[Selection Macros]]
### [[Representations]]
#### [[Lines]]
#### [[Sticks]]
#### [[Cartoon]]
#### [[Surface]]
#### [[Mesh]]
#### [[Spheres]]
#### [[Dots]]
### [[Color]]
### [[Displaying biochemical properties]]
## [[Display Settings]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
## [[Scenes]]
## [[Mouse Settings]]
## [[Wizards]]
## [[Plugins]]
## [[Ray-tracing]]
## [[Settings Reference (all settings and what they do)]]
## [[Movies and Animations]]
## [[Structure Alignment]]
## [[Structure Alignment Editor]]
# [[:Category:Commands|Command Language]] (I added a sample category. Should we continue with something like this?) [[User:Cmoad|Charlie]]
## [[PyMOL Command Script]]
## [[PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Example Scripts]]
## [[Script Library]]
# [[:Category:Plugins]]
## [[List of Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Category:Plugins

2005-02-17T21:43:33Z

Cmoad:

A list of available plugins written by the community, for the community.

PDB Loader Service

2005-02-17T21:42:49Z

Cmoad:

==Description==
Originally bundled with PyMol 0.96, the PDB Loader Service plugin dynamically downloads a requested PDB from [http://www.rcsb.org/pdb/ RCSB] and displays it in PyMol.
==Comments==
Although the plugin is completely functional, I have written newer versions which never touch the filesystem and as a result are much cleaner. See the [[Tutorial on writing plugins]] for one such example.
==Author==
[[User:Cmoad|Charlie]] Moad

[[Category:Plugins]]

Main Page

2005-02-17T20:52:43Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* A wiki edit/user policy is needed.
* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:Discussion|Discussion]]
## [[:Category:PyMOL Beta|The Bleeding Edge]]
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Using the GUI]]
## [[Launching PyMOL]]
### [[Command Line Options]]
### [[Launching From a Script]]
## [[Mouse Controls]]
## [[Objects and Selections]]
### [[Working with Objects]]
### [[Working with Selections]]
### [[Selector Quick Reference]]
#### [[Single-word Selectors]]
#### [[Property Selectors]]
#### [[Selection Algebra]]
#### [[Selection Macros]]
### [[Representations]]
#### [[Lines]]
#### [[Sticks]]
#### [[Cartoon]]
#### [[Surface]]
#### [[Mesh]]
#### [[Spheres]]
#### [[Dots]]
### [[Color]]
### [[Displaying biochemical properties]]
## [[Display Settings]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
## [[Scenes]]
## [[Mouse Settings]]
## [[Wizards]]
## [[Plugins]]
## [[Ray-tracing]]
## [[Settings Reference (all settings and what they do)]]
## [[Movies and Animations]]
## [[Structure Alignment]]
## [[Structure Alignment Editor]]
# [[:Category:Commands|Command Language]] (I added a sample category. Should we continue with something like this?) [[User:Cmoad|Charlie]]
## [[PyMOL Command Script]]
## [[PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Example Scripts]]
## [[Script Library]]
# [[Plugins]]
## [[List of Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Rms

2005-02-17T17:17:13Z

Cmoad:

===DESCRIPTION===
"rms" computes a RMS fit between two atom selections, but does not
tranform the models after performing the fit.

===USAGE===
rms (selection), (target-selection)

===EXAMPLES===
fit ( mutant and name ca ), ( wildtype and name ca )

===SEE ALSO===
[[Cmd fit|fit]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_fit|intra_fit]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]]

[[Category:Commands|rms]]

Fit

2005-02-17T17:15:20Z

Cmoad:

===DESCRIPTION===
"fit" superimposes the model in the first selection on to the model
in the second selection. Only matching atoms in both selections
will be used for the fit.

===USAGE===
fit (selection), (target-selection)

===EXAMPLES===
fit ( mutant and name ca ), ( wildtype and name ca )

===SEE ALSO===
[[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_fit|intra_fit]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]]

[[Category:Commands|fit]]

Fit

2005-02-17T17:15:04Z

Cmoad:

Align

2005-02-17T17:13:27Z

Cmoad:

===DESCRIPTION===
"align" performs a sequence alignment followed by a structural
alignment, and then carrys out zero or more cycles of refinement
in order to reject structural outliers found during the fit.

===USAGE===
align (source), (target) [,cutoff [,cycles [,gap [,extend \
[,skip [,object [,matrix [, quiet ]]]]]]]]

===PYMOL API===
cmd.align( string source, string target, float cutoff=2.0,
int cycles=2, float gap=-10.0, float extend=-0.5,
float extend=-0.5,int skip=0, string object=None,
string matrix="BLOSUM62",int quiet=1 )

===NOTE===
If object is not None, then align will create an object which
indicates which atoms were paired between the two structures

===EXAMPLES===
align prot1////CA, prot2, object=alignment

===SEE ALSO===
[[Cmd fit|fit]], [[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]]

[[Category:Commands|align]]

Align

2005-02-17T17:13:11Z

Cmoad:

===DESCRIPTION===
"align" performs a sequence alignment followed by a structural
alignment, and then carrys out zero or more cycles of refinement
in order to reject structural outliers found during the fit.

===USAGE===
align (source), (target) [,cutoff [,cycles [,gap [,extend \
[,skip [,object [,matrix [, quiet ]]]]]]]]

===PYMOL API===
cmd.align( string source, string target, float cutoff=2.0,
int cycles=2, float gap=-10.0, float extend=-0.5,
float extend=-0.5,int skip=0, string object=None,
string matrix="BLOSUM62",int quiet=1 )

===NOTE===
If object is not None, then align will create an object which
indicates which atoms were paired between the two structures

===EXAMPLES===
align prot1////CA, prot2, object=alignment

===SEE ALSO===
[[Cmd fit|fit]], [[Cmd rms|rms]], [[Cmd rms_cur|rms_cur]], [[Cmd intra_rms|intra_rms]], [[Cmd intra_rms_cur|intra_rms_cur]], [[Cmd pair_fit|pair_fit]]

[[Category:Commands]]

Extend

2005-02-17T17:07:32Z

Cmoad:

===DESCRIPTION===
"extend" is an API-only function which binds a new external
function as a command into the PyMOL scripting language.

===PYMOL API===
cmd.extend(string name,function function)

===PYTHON EXAMPLE===
def foo(moo=2): print moo
cmd.extend('foo',foo)

The following would now work within PyMOL:
PyMOL>foo
2
PyMOL>foo 3
3
PyMOL>foo moo=5
5
PyMOL>foo ?

Usage: foo [ moo ]

===NOTES===
For security reasons, new PyMOL commands created using "extend" are
not saved or restored in sessions.

===SEE ALSO===
[[Cmd alias|alias]], [[Cmd api|api]]

[[Category:Commands|extend]]

Alias

2005-02-17T17:04:58Z

Cmoad:

===DESCRIPTION===
"alias" allows you to bind a commonly used command to a single PyMOL keyword.

===USAGE===
alias name, command-sequence

===PYMOL API===
cmd.alias(string name,string command)

===EXAMPLES===
alias go,load $TUT/1hpv.pdb; zoom 200/; show sticks, 200/ around 8
go

===NOTES===
For security reasons, new PyMOL commands created using "extend" are not saved or restored in sessions.

===SEE ALSO===
[[Cmd extend|extend]], [[Cmd api|api]]

[[Category:Commands|alias]]

Alias

2005-02-17T16:53:49Z

Cmoad:

DESCRIPTION

"alias" allows you to bind a commonly used command to a single PyMOL keyword.

USAGE

alias name, command-sequence

PYMOL API

cmd.alias(string name,string command)

EXAMPLES

alias go,load $TUT/1hpv.pdb; zoom 200/; show sticks, 200/ around 8
go

NOTES

For security reasons, new PyMOL commands created using "extend" are
not saved or restored in sessions.

SEE ALSO

extend, api

[[Category:Commands|alias|alias]]

Category:Commands

2005-02-17T16:52:52Z

Cmoad:

This is a list of all commands for PyMol's interface and cmd module.

Main Page

2005-02-17T16:51:43Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

=== Layout Schema ===
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Graphics]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
# [[Basic Usage (controls, rendering, selections)]]
## [[Launching PyMOL (has been asked often)]]
## [[Interface]]
### [[Mouse Controls]]
## [[Atom Selections]]
## [[Concepts/Basics of displaying molecules]]
### [[Cartoon Representations]]
### [[Rendering molecules]]
#### [[Coloring molecules]]
#### [[Displaying biochemical properties]]
## [[:Category:Commands|Command Language]]
## [[Ray-tracing]]
## [[Movies and Animations]]
### [[Scenes]]
## [[Settings Reference (all settings and what they do)]]
## [[Structure Alignment]]
### [[Structure Alignment Editor]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Script Library]]
## [[Some kind of "script collection" would be very useful]]
# [[Plugins]]
## [[List of Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Alias

2005-02-17T16:51:08Z

Cmoad:

Alias

2005-02-17T16:50:11Z

Cmoad:

Alias

2005-02-17T16:49:09Z

Cmoad:

Alias

2005-02-17T16:48:12Z

Cmoad:

Main Page

2005-02-17T16:47:10Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

=== Layout Schema ===
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Graphics]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
# [[Basic Usage (controls, rendering, selections)]]
## [[Launching PyMOL (has been asked often)]]
## [[Interface]]
### [[Mouse Controls]]
## [[Atom Selections]]
## [[Concepts/Basics of displaying molecules]]
### [[Cartoon Representations]]
### [[Rendering molecules]]
#### [[Coloring molecules]]
#### [[Displaying biochemical properties]]
## [[:Commands|Command Language]]
## [[Ray-tracing]]
## [[Movies and Animations]]
### [[Scenes]]
## [[Settings Reference (all settings and what they do)]]
## [[Structure Alignment]]
### [[Structure Alignment Editor]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Script Library]]
## [[Some kind of "script collection" would be very useful]]
# [[Plugins]]
## [[List of Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Alias

2005-02-17T16:46:27Z

Cmoad:

Main Page

2005-02-17T16:44:09Z

Cmoad: /* Layout Schema */

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

=== Helping ===
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

* Wiki schema/design/organization: Below you'll find the current layout design
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* Smoothing out the edges: Editors are needed just to fix our typos!
* Etc...

=== Editors Needed ===
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

We need your help. So join today & happy editing!

[[User:Tree|Tree]]
== Section Layout ==
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

=== Layout Schema ===
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Graphics]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
# [[Basic Usage (controls, rendering, selections)]]
## [[Launching PyMOL (has been asked often)]]
## [[Interface]]
### [[Mouse Controls]]
## [[Atom Selections]]
## [[Concepts/Basics of displaying molecules]]
### [[Cartoon Representations]]
### [[Rendering molecules]]
#### [[Coloring molecules]]
#### [[Displaying biochemical properties]]
## [[:Category:Commands|Command Language]]
## [[Ray-tracing]]
## [[Movies and Animations]]
### [[Scenes]]
## [[Settings Reference (all settings and what they do)]]
## [[Structure Alignment]]
### [[Structure Alignment Editor]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Script Library]]
## [[Some kind of "script collection" would be very useful]]
# [[Plugins]]
## [[List of Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

User:Cmoad

2005-02-17T16:36:33Z

Cmoad:

==whoami==
Charles Moad
Research Associate
[http://sda.iu.edu Scientific Data Analysis Lab]
[http://ptl.iu.edu Pervasive Technology Labs]
[http://www.indiana.edu Indiana University]

[[User:Cmoad|Charlie]] 10:36, 17 Feb 2005 (CST)

User:Cmoad

2005-02-17T16:31:26Z

Cmoad:

==whoami==
Charles Moad
Research Associate
[http://sda.iu.edu Scientific Data Analysis Lab]
[http://ptl.iu.edu Pervasive Technology Labs]
[http://www.indiana.edu Indiana University]