This is a read-only mirror of pymolwiki.org

Difference between revisions of "Main Page"

From PyMOL Wiki
Jump to navigation Jump to search
(spectrum_states)
m (2 revisions)
 
(124 intermediate revisions by 12 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__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.
 
| 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]]'')
 
||'''[[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 & Updates
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|-
 
|-
−
! New Script
+
! Official Release
−
| [[spectrum_states]] colors states of multi-state object
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
−
! New Script
+
! Python 3
−
| [[TMalign]] is a wrapper for the TMalign program
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
−
! Gallery Updates
+
! POSF
−
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
−
! New Script
+
! Tutorial
−
| [[save_settings]] can dump all changed settings to a file
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
−
! Tips & Tricks
+
! New Plugin
−
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
+
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
|-
 
|-
−
! Wiki Update
+
! Selection keywords
−
| Wiki has been updated. Please report any problems to the sysops.
+
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! New Scripts
+
! Plugin Update
−
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
+
| [[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
−
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. 
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
−
|-
 
−
! 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
 
! Older News
Line 63: Line 61:
 
|-
 
|-
 
|<div class="didyouknow" >
 
|<div class="didyouknow" >
−
<DPL>
+
<DynamicPageList>
−
namespace=
+
randomcount=1
 
category=Commands|Plugins|Script_Library|Settings
 
category=Commands|Plugins|Script_Library|Settings
 
includepage=*
 
includepage=*
−
includemaxlength=450
+
includemaxlength=1050
 
escapelinks=false
 
escapelinks=false
 +
allowcachedresults=false
 
resultsheader=__NOTOC__ __NOEDITSECTION__
 
resultsheader=__NOTOC__ __NOEDITSECTION__
−
randomcount=1
 
−
mode=userformat
 
−
addpagecounter=true
 
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
−
</DPL>
+
</DynamicPageList>
 
</div>
 
</div>
 
<div style="clear: both;"></div>
 
<div style="clear: both;"></div>
Line 80: Line 76:
 
|
 
|
 
|style="vertical-align: top; width: 18%"|
 
|style="vertical-align: top; width: 18%"|
−
<DPL>
+
<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
randomcount=1
Line 87: Line 83:
 
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
ordermethod=none
 
ordermethod=none
−
</DPL>
+
allowcachedresults=false
 +
</DynamicPageList>
  
 
|}
 
|}

Latest revision as of 03:21, 22 June 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...

Ribbon smooth

==Overview==

This PyMOL setting determines smoothly how PyMOL draws ribbons. Turning on the setting smooths out the ribbons and make the image look cleaner. The setting is by default off, and yet, when turned on shows absolutely no decreased performance.

Usage

#show ribbons, first
hide; show ribbon

# turn on smoothing
set ribbon_smooth, 1

# turn off smoothing
set ribbon_smooth, 0
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=14896"