Difference between revisions of "Main Page"

	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.importing

Latest revision as of 03:21, 22 June 2021

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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...

Load aln

load_aln loads a pairwise sequence alignment file as an alignment object into PyMOL.

Installation

load_aln is available from the psico package and requires biopython.

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install biopython

Usage

load_aln filename [, object [, mobile [, target
    [, mobile_id [, target_id [, format [, transform ]]]]]]]

Arguments

filename = str: alignment file
object = str: name of the object {default: filename prefix}
mobile, target = str: atom selections {default: ids from alignment file}
mobile_id, target_id = str: ids from alignment file {default: first two}
format = str: file format, see http://biopython.org/wiki/AlignIO {default: guess from first line in file}
transform = 0/1: superpose mobile on target (using fit) {default: 0}

== ..→

A Random PyMOL-generated Cover. See Covers.

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-|+ 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/]]
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+|}
+{| align="center" style="padding-bottom: 3em;"
+|+ 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.
-|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
-| New accounts: email jason (dot) vertrees (@) gmail dot com
+| To request a new account, email SBGrid at:  accounts (@) sbgrid dot 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" 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: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
+| style="font-size: 1.1em; 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]]'''
+| 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]]'''
+| 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]]'')
-||'''[[GoogleSearch]]'''
+||'''[[PyMOL_mailing_list|Getting Help]]'''
 |}
@@ Line 25: / Line 29: @@
 |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
 |-
-! New Plugin
+! Official Release
-| [[Contact_Map_Visualizer]] visualize residues corresponding to its contact map
+| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 |-
-! New Script
+! Python 3
-| [[spectrum_states]] colors states of multi-state object
+| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 |-
-! New Script
+! POSF
-| [[TMalign]] is a wrapper for the TMalign program
+| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 |-
-! Gallery Updates
+! Tutorial
-| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
+| [[Plugins Tutorial]] updated for PyQt5
 |-
-! New Script
+! New Plugin
-| [[save_settings]] can dump all changed settings to a file
+| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
-|-
-! Tips & Tricks
-| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
-|-
-! Wiki Update
-| Wiki has been updated. Please report any problems to the sysops.
 |-
-! New Scripts
+! Selection keywords
-| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
+| 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
-| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
+| [[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
-| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]].
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
-|-
-! New Script
-| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
 |-
 ! Older News
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