Difference between revisions of "Main Page"

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(added information about the new plugin MOLE for PyMOL)
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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!
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|+ 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;"
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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.
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
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| New accounts: email jason (dot) vertrees (@) gmail dot com
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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
 
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{| 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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{| 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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|-  
 
|-  
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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]]'''
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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]]'''
 
|-
 
|-
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| 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]]'''
 
|-
 
|-
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| 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]]'')
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||'''[[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
 
|-
 
|-
−
! New Plugin
+
! Selection keywords
−
| [[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 [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
−
|-
 
−
! 3D using Geforce
 
−
| 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.
 
−
|-
 
−
! New Plugin
 
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
 
 
|-
 
|-
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! New Software
+
! Official Release
−
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
+
| [https://pymol.org PyMOL v2.0 has been released] on September 20, 2017.
 
|-
 
|-
−
! New Script
+
! Plugin Update
−
| [[cgo_arrow]] draws an arrow between two picked atoms.
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
−
! Tips & Tricks
+
! Official Release
−
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
+
| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
 
|-
 
|-
−
! New Script
+
! Official Release
−
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
+
| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
 
|-
 
|-
 
! New Script
 
! New Script
−
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
−
! New Script
+
! New Plugin
−
| [[DistancesRH|Distances RH]]
+
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
|-
 
|-
−
! 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 v1.8.0 has been released] on Nov 18, 2015.
 
|-
 
|-
−
! OS X Compatibility
+
! PyMOL Open-Source Fellowship
−
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
+
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
|-
 
|-
−
! New Script
+
! Official Release
−
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
+
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
|-
 
|-
−
! New Script
+
! New Plugin
−
| [[b2transparency]] can set surface transparency based on atom b-factor
+
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
−
|-
 
−
! 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
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
−
|-
 
−
! New Script
 
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| [[set_phipsi]] can set phi/psi angles for all residues in a selection
 
−
|-
 
−
! New Script
 
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| [[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.
 
−
|-
 
−
! New Script
 
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| [[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!
 
−
|-
 
−
! New Script
 
−
| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
+
| [[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
−
| [[spectrum_states]] colors states of multi-state object
+
| 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.
−
|-
 
−
! 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
 
! Older News
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
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Revision as of 12:30, 7 February 2018

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
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Official Release PyMOL v2.0 has been released on September 20, 2017.
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
Official Release PyMOL v1.8.6 has been released on March 9, 2017.
Official Release PyMOL v1.8.4 has been released on October 4, 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...

Tiff2ccp4

= Overview =

This script will convert tiff stacks to CCP4 maps for reading in PyMOL.

See also the load_img_stack script for loading image stacks directly into PyMOL.

If someone knows how to determine the file's dimensions from the file itself (not the image size, but the physical dimension size) please let me know.

Note: requires Python 2.7 or later (for argparse).

Usage

#
# convert input.tiff to output.ccp4 which has cell dimensions
# x=40 A, y=80.5 A, Z=125.2 A
#
python tiff2ccp4.py input.tiff output.ccp4 -x 40 -y 80.5 -z 125.2

#
# print help
#
python tiff2ccp4.py -h

The Code

<source lang="python">

  2. tiff2ccp4.py -- convert a TIFF stack to a CCP4 map
  4. Author: Jason Vertrees
  5. Date : 2011-09-16
  7. Notes : To get help, type "python tiff2ccp4.py -h"

import struct import sys import string

  1. key = field_type
  2. value = # bytes for that field

field_types = ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12731"