Difference between revisions of "Main Page"

Type	Python Module
Download	uniprot_features.py
Author(s)	Thomas Holder
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

Revision as of 12:08, 15 September 2016

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 v1.8.2 has been released on April 20, 2016.
New Script	dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin	LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release	PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship	Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release	PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin	PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin	Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin	MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce	PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
Older News	See Older News.

Did you know...

Uniprot features

uniprot_features fetches the sequence annotation (features) from uniprot.org and create named selections for each feature.

Requires residue numbering (resi) to match uniprot sequence!

Usage

uniprot_features uniprot_id [, selection [, withss [, prefix ]]]

Example

Show the active site of human pepsin A:

fetch 1flh, async=0

# fix residue numbering to match uniprot sequence
alter all, resi=resv+62

# create selections
uniprot_features PEPA4_HUMAN

# show sticks for active site
as cartoon
set cartoon_side_chain_helper
show sticks, feature_active_site
zoom feature_active_site

@@ Line 1: / Line 1: @@
 __NOTOC__
-{| align="center" style="padding-bottom: 4em;"
+{| align="center" style="padding-bottom: 3em;"
 |+ 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;"
+|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; 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-family: 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;"
+|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-family: 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;"
 |+ 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
@@ Line 17: / Line 18: @@
 | 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]]'''
+||'''[[PyMOL_mailing_list|Getting Help]]'''
 |}
@@ Line 25: / Line 26: @@
 |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
 |-
-! PyMOL on the iPad
+! Official Release
-| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
+| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
-|-
-! OS X Compatibility
-| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
-|-
-! New Script
-| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
-|-
-! New Script
-| [[b2transparency]] can set surface transparency based on atom b-factor
-|-
-! New Extension
-| [[psico]] is a python module which extends PyMOL with many commands
 |-
 ! New Script
-| [[uniprot_features]] makes named selections for sequence annotations from uniprot
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 |-
 ! New Plugin
-| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 |-
-! New Script
+! Official Release
-| [[set_phipsi]] can set phi/psi angles for all residues in a selection
+| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 |-
-! New Script
+! PyMOL Open-Source Fellowship
-| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
+| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 |-
-! New Script
+! Official Release
-| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
+| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 |-
-! New Script
+! New Plugin
-| [[cyspka]] is an experimental surface cysteine pKa predictor.
+| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 |-
 ! New Plugin
-| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 |-
-! New Script
+! New Plugin
-| [[spectrum_states]] colors states of multi-state object
+| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
 |-
-! New Script
+! 3D using Geforce
-| [[TMalign]] is a wrapper for the TMalign program
+| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
-|-
-! Gallery Updates
-| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
-|-
-! New Script
-| [[save_settings]] can dump all changed settings to a file
-|-
-! 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
-| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
-|-
-! New Script
-| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
-|-
-! 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]].
-|-
-! 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
@@ Line 99: / Line 64: @@
 |-
 |<div class="didyouknow" >
-<DPL>
+<DynamicPageList>
-namespace=
+randomcount=1
 category=Commands|Plugins|Script_Library|Settings
 includepage=*
-includemaxlength=450
+includemaxlength=1050
 escapelinks=false
+allowcachedresults=false
 resultsheader=__NOTOC__ __NOEDITSECTION__
-randomcount=1
-mode=userformat
-addpagecounter=true
 listseparators=,<h3>[[%PAGE%]]</h3>,,\n
-</DPL>
+</DynamicPageList>
 </div>
 <div style="clear: both;"></div>
@@ Line 116: / Line 79: @@
 |
 |style="vertical-align: top; width: 18%"|
-<DPL>
+<DynamicPageList>
 imagecontainer=Covers
 randomcount=1
@@ Line 123: / Line 86: @@
 listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 ordermethod=none
-</DPL>
+allowcachedresults=false
+</DynamicPageList>
 |}

Difference between revisions of "Main Page"

Revision as of 12:08, 15 September 2016

Uniprot features

Usage

Example

See also

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