Difference between revisions of "Main Page"

Type	PyMOL Plugin
Download	plugins/dynoplot.py
Author(s)	Dan Kulp
License	-
	This code has been put under version control in the project Pymol-script-repo

Revision as of 22:16, 26 February 2021

hosted by

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 v2.4 has been released on May 20, 2020.
Python 3	New Python 3 compatibility guide for scripts and plugins
Official Release	PyMOL v2.3 has been released on February 11, 2019.
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...

DynoPlot

Introduction

This script was setup to do generic plotting, that is given a set of data and axis labels it would create a plot. Initially, I had it setup to draw the plot directly in the PyMol window (allowing for both 2D and 3D style plots), but because I couldn't figure out how to billboard CGO objects (Warren told me at the time that it couldn't be done) I took a different approach. The plot now exists in it's own window and can only do 2D plots. It is however interactive. I only have here a Rama.(phi,psi) plot, but the code can be easily extended to other types of data. For instance, I had this working for an energy vs distance data that I had generated by another script.

This script will create a Phi vs Psi(Ramachandran) plot of the selection given. The plot will display data points which can be dragged around Phi,Psi space with the corresponding residue's Phi,Psi angles changing in the ..→

A Random PyMOL-generated Cover. See Covers.

@@ Line 1: / Line 1: @@
 __NOTOC__
-{| align="center" style="padding-bottom: 4em;"
+{| 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;"
+|}
+{| 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;"
+|- 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;"
-|+ 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
+{| 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;"
+|+ 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]]'''
+| 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
 |-
-! 3D using Geforce
+! Official Release
-| 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.
+| [https://pymol.org PyMOL v2.4 has been released] on May 20, 2020.
-|-
-! New Plugin
-| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
-|-
-! New Software
-| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
-|-
-! New Script
-| [[cgo_arrow]] draws an arrow between two picked atoms.
-|-
-! Tips & Tricks
-| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
-|-
-! New Script
-| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
-|-
-! New Script
-| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
-|-
-! New Script
-| [[DistancesRH|Distances RH]]
-|-
-! PyMOL on the iPad
-| 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.
 |-
-! OS X Compatibility
+! Python 3
-| 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 [[2to3|Python 3 compatibility guide]] for scripts and plugins
 |-
-! New Script
+! Official Release
-| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
+| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
 |-
-! New Script
+! POSF
-| [[b2transparency]] can set surface transparency based on atom b-factor
+| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 |-
-! New Extension
+! Tutorial
-| [[psico]] is a python module which extends PyMOL with many commands
+| [[Plugins Tutorial]] updated for PyQt5
-|-
-! New Script
-| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 |-
 ! New Plugin
-| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 |-
-! New Script
+! Selection keywords
-| [[set_phipsi]] can set phi/psi angles for all residues in a selection
+| 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
-| [[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.
+| [[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
-| [[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!
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
-|-
-! New Script
-| [[cyspka]] is an experimental surface cysteine pKa predictor.
-|-
-! New Plugin
-| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
-|-
-! New Script
-| [[spectrum_states]] colors states of multi-state object
-|-
-! New Script
-| [[TMalign]] is a wrapper for the TMalign program
-|-
-! 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 123: / Line 64: @@
 |-
 |<div class="didyouknow" >
-<DPL>
+<DynamicPageList>
-namespace=
+randomcount=1
 category=Commands|Plugins|Script_Library|Settings
 includepage=*
 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 140: / Line 79: @@
 |
 |style="vertical-align: top; width: 18%"|
-<DPL>
+<DynamicPageList>
 imagecontainer=Covers
 randomcount=1
@@ Line 147: / 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 22:16, 26 February 2021

DynoPlot

Introduction

Navigation menu

Search