Difference between revisions of "Main Page"

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__NOTOC__
 
__NOTOC__
{| align="center" style="padding-bottom: 4em;"
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{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
+
|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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{| align="center" style="padding-bottom: 3em;"
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|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
 +
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
 +
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
 +
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
 +
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
 
|}
 
|}
{| 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;"
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|+ 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
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{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
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|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; 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]]'''
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; 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]]'''
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; 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]]'''
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|-
 
|-
! Search
+
! Official Release
| [[GoogleSearch]] widget fixed.
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
 
! 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
+
! Python 3
| [[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 [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
! New Script
+
! POSF
| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
! New Scripts
+
! Tutorial
| [[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.
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
! New Script
+
! New Plugin
| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
+
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
|-
 
|-
! New Script
+
! Selection keywords
| See [[Supercell]], the new script for making XxYxZ supercells.
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
! New Script
+
! Plugin Update
| 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.
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
 
! New Script
 
! New Script
| See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
 
! 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
+
! Older News
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
+
| See [[Older_News|Older News]].
 
|}
 
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
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Latest revision as of 12:11, 10 May 2021

hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

Draw

Showing Draw in Action

Draw creates an oversized and antialiased OpenGL image using the current window. It's like Ray but not ray traced. Also, as now with Ray the oversized images are scaled and shown in the viewer window. As Draw doesn't ray trace the shadows of the scene, it is far faster than ray.

Usage

draw [ width [, height [, antialias ]]]

Examples

draw 1600

will create an 1600-pixel wide image with an aspect ratio equal to that of the current screen.

draw 2000, 1500, 0

will create a 2000 by 1500 pixel image with antialiasing disabled

draw 600, 400, 2

will create a 600 by 500 pixel image with maximum (16X) antialiasing

Match ray tracing appearance

Since PyMOL 1.6, all "line"-type representations can be rendered as cylinders if shaders are available and all *_as_cylinders settings are set. Example:

set line_as_cylinders
set nonbonded_as_cylinders
set ribbon_as_cylinders
set mesh_as_cylinders
set dash_as_cylinders
 ..→
A Random PyMOL-generated Cover. See Covers.