PyMOL Wiki - User contributions [en]

Connect mode

2012-12-04T04:27:01Z

Nipsy:

= Overview =
Sets how bonds are made when loading a file.

Values:
* 0 = distance-based and CONECT records
* 1 = CONECT records
* 2 = distance-based, ignores CONECT records
* 3 = CONECT records and distance

= Syntax =
<source lang="python">
# ignore CONECT records
set connect_mode, 2

</source>

= See Also =
[[Load]], [[Connect_cutoff]], [[Connect_bonded]]

[[Category:Settings]]

Connect mode

2012-12-04T04:26:52Z

Nipsy:

Connect mode

2012-12-04T04:26:38Z

Nipsy:

Connect mode

2012-12-03T23:11:00Z

Nipsy:

Connect mode

2012-12-03T23:10:50Z

Nipsy:

Main Page

2010-03-30T08:16:16Z

Nipsy:

__NOTOC__
{| align="center" style="padding-bottom: 4em;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|}
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! fetch_host setting
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
|-
! Fetch
| [[Fetch]] has been updated to also load electron density maps.
|-
! Schrodinger Buys PyMOL
| Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].
|-
! User Movie
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL.
|-
! New setting
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
|-
! Search fixed.
| Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
|-
! New Command
| [[Cache]]—stores information on structures, so we don't have to recompute them.
|-
! Warren
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
|-
! Setting
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
|-
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
|-
! New Script
| [[ContactsNCONT]]—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
|-
! Fun
| [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).
|-
! PyMOLWiki
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
|-
! PyMOLWiki
| New — Search the PyMOLWiki via [[GoogleSearch]]
|-
! PyMOL
| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
|-
! PyMOL
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DPL>
namespace=
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=450
escapelinks=false
resultsheader=__NOTOC__ __NOEDITSECTION__
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addpagecounter=true
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DPL>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<DPL>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
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</DPL>

|}

Main Page

2010-03-30T07:59:35Z

Nipsy:

Main Page

2010-03-30T07:43:33Z

Nipsy:

__NOTOC__
{| align="center" style="padding-bottom: 4em;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|}
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! fetch_host setting
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
|-
! Fetch
| [[Fetch]] has been updated to also load electron density maps.
|-
! Schrodinger Buys PyMOL
| Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].
|-
! User Movie
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL.
|-
! New setting
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
|-
! Search fixed.
| Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
|-
! New Command
| [[Cache]]—stores information on structures, so we don't have to recompute them.
|-
! Warren
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
|-
! Setting
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
|-
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
|-
! New Script
| [[ContactsNCONT]]—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
|-
! Fun
| [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).
|-
! PyMOLWiki
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
|-
! PyMOLWiki
| New — Search the PyMOLWiki via [[GoogleSearch]]
|-
! PyMOL
| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
|-
! PyMOL
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DPL>
namespace=
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=450
escapelinks=false
resultsheader=__NOTOC__ __NOEDITSECTION__
randomcount=1
mode=userformat
addpagecounter=true
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DPL>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<dpl>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
</dpl>

|}

Main Page

2010-03-30T07:38:35Z

Nipsy:

__NOTOC__
{| align="center" style="padding-bottom: 4em;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|}
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! fetch_host setting
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
|-
! Fetch
| [[Fetch]] has been updated to also load electron density maps.
|-
! Schrodinger Buys PyMOL
| Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].
|-
! User Movie
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL.
|-
! New setting
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
|-
! Search fixed.
| Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
|-
! New Command
| [[Cache]]—stores information on structures, so we don't have to recompute them.
|-
! Warren
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
|-
! Setting
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
|-
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
|-
! New Script
| [[ContactsNCONT]]—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
|-
! Fun
| [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).
|-
! PyMOLWiki
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
|-
! PyMOLWiki
| New — Search the PyMOLWiki via [[GoogleSearch]]
|-
! PyMOL
| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
|-
! PyMOL
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<dpl>
namespace=
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=450
escapelinks=false
resultsheader=__NOTOC__ __NOEDITSECTION__
randomcount=1
mode=userformat
addpagecounter=true
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</dpl>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<dpl>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
</dpl>

|}

Main Page

2010-03-30T07:37:43Z

Nipsy:

__NOTOC__
{| align="center" style="padding-bottom: 4em;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|}
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! fetch_host setting
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
|-
! Fetch
| [[Fetch]] has been updated to also load electron density maps.
|-
! Schrodinger Buys PyMOL
| Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].
|-
! User Movie
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL.
|-
! New setting
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
|-
! Search fixed.
| Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
|-
! New Command
| [[Cache]]—stores information on structures, so we don't have to recompute them.
|-
! Warren
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
|-
! Setting
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
|-
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
|-
! New Script
| [[ContactsNCONT]]—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
|-
! Fun
| [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).
|-
! PyMOLWiki
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
|-
! PyMOLWiki
| New — Search the PyMOLWiki via [[GoogleSearch]]
|-
! PyMOL
| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
|-
! PyMOL
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DPL>
namespace=
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=450
escapelinks=false
resultsheader=__NOTOC__ __NOEDITSECTION__
randomcount=1
mode=userformat
addpagecounter=true
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DPL>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<dpl>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
</dpl>

|}

Template:Extension DPL

2010-03-30T06:50:14Z

Nipsy: Template:Extension DPL

<noinclude>This page was automatically created. It serves as an anchor page for all '''[[Special:WhatLinksHere/Template:Extension_DPL|invocations]]''' of [http://mediawiki.org/wiki/Extension:DynamicPageList Extension:DynamicPageList (DPL)].</noinclude>