Difference between revisions of "Main Page"

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__NOTOC__
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{| 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.
 +
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
 +
|
 +
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
 +
| For Educational downloads go to http://pymol.org/educational
 +
|}
 +
{| 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
 +
|-
 +
! New Script
 +
| [[ColorByDisplacement]] Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.
 +
|-
 +
! New Script
 +
| [[DisplacementMap]] Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
 +
|-
 +
! New Script
 +
| Two new scripts: [[AAindex]] and [[Sidechaincenters]]
 +
|-
 +
! New Plugin
 +
| [[CAVER_2.0]] update to the CAVER plugin.
 +
|-
 +
! New Script
 +
| [[AngleBetweenHelices]] calculates the angle between two helices.
 +
|-
 +
! Search
 +
| [[GoogleSearch]] widget fixed.
 +
|-
 +
! New Script
 +
| [[Spectrumany]] creates color gradients with arbitrary color sequences.
 +
|-
 +
! New Script
 +
| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
 +
|-
 +
! New Script
 +
| [[Center Of Mass]] has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). 
 +
|-
 +
! New Script
 +
| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
 +
|-
 +
! New Scripts
 +
| [[ResDe]] is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
 +
|-
 +
! New Script
 +
| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
 +
|-
 +
! New Script
 +
| See [[Supercell]], the new script for making XxYxZ supercells.
 +
|-
 +
! New Script
 +
| See [[Split_Object_Along_Axis]], for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
 +
|-
 +
! New Script
 +
| See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
 +
|-
 +
! Server updates
 +
| The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend.  We are now fully functional.  A '''deep''' thanks to [http://www.bitgnome.net BitGnome] for donating time and hardware for the PyMOL project.
 +
|-
 +
! 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.
 +
|}
 +
|style="vertical-align: top; width: 40%"|
 +
{| class="jtable" style="float: right; width: 90%"
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
 +
|-
 +
|<div class="didyouknow" >
 +
<DPL>
 +
namespace=
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category=Commands|Plugins|Script_Library|Settings
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includepage=*
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includemaxlength=450
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escapelinks=false
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resultsheader=__NOTOC__ __NOEDITSECTION__
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randomcount=1
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addpagecounter=true
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listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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</DPL>
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</div>
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<div style="clear: both;"></div>
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|}
 +
|
 +
|style="vertical-align: top; width: 18%"|
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<DPL>
 +
imagecontainer=Covers
 +
randomcount=1
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escapelinks=false
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openreferences=true
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
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ordermethod=none
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</DPL>
  
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|}
 
 
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==<center>[http://mysearchends.com/SESS_478OTN8fDEyOTYwODM1Mzd8fDE5MDZ8fChFTkdJTkUpIE1lZGlhV2lraQ%3D%3D_.html <big>'''<u>>>>  <<<</u>'''</big>]</center>==
 
 
 
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Revision as of 14:03, 27 January 2011

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
For Educational downloads go to http://pymol.org/educational
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch
News & Updates
New Script ColorByDisplacement Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.
New Script DisplacementMap Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
New Script Two new scripts: AAindex and Sidechaincenters
New Plugin CAVER_2.0 update to the CAVER plugin.
New Script AngleBetweenHelices calculates the angle between two helices.
Search GoogleSearch widget fixed.
New Script Spectrumany creates color gradients with arbitrary color sequences.
New Script BbPlane will draw CGO planes across the backbone highlighting planarity of arrangement.
New Script Center Of Mass has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere).
New Script Jump is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
New Scripts ResDe is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
New Script See BiologicalUnit, for a workaround to the buggy Symexp command or if you just want to learn more about symmetry expansion in PyMOL.
New Script See Supercell, the new script for making XxYxZ supercells.
New Script See Split_Object_Along_Axis, for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
New Script See Consistent_View/_Map_Inspect, which is a toolkit for rapidly inspecting multiple maps and models.
Server updates The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend. We are now fully functional. A deep thanks to BitGnome for donating time and hardware for the PyMOL project.
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 sale.
User Movie One of our users has posted another 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'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.
Did you know...

The DPL extension (version 2.3.0) produced a SQL statement which lead to a Database error.
The reason may be an internal error of DPL or an error which you made,
especially when using DPL options like titleregexp.
Query text is:
SELECT DISTINCT `pmw_page`.page_namespace AS page_namespace,`pmw_page`.page_title AS page_title,`pmw_page`.page_id AS page_id, `pmw_page`.page_title AS sortkey, `pmw_page`.page_counter AS page_counter FROM `pmw_page` INNER JOIN `pmw_categorylinks` AS cl0 ON `pmw_page`.page_id=cl0.cl_from AND (cl0.cl_to='Commands' OR cl0.cl_to='Plugins' OR cl0.cl_to='Script_Library' OR cl0.cl_to='Settings') WHERE 1=1 AND `pmw_page`.page_namespace IN ('0') AND `pmw_page`.page_is_redirect=0 ORDER BY page_title ASC LIMIT 500 OFFSET 0

Error message is:


A Random PyMOL-generated Cover. See Covers.