Difference between revisions of "Main Page"

Type	Python Script
Download	ccp4_ncont.py
Author(s)	Gerhard Reitmayr and Dalia Daujotyte
License	GPL
	This code has been put under version control in the project Pymol-script-repo

Revision as of 06:57, 27 November 2018

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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
POSF	New PyMOL fellows announced for 2018-2019
Tutorial	Plugins Tutorial updated for PyQt5
Official Release	PyMOL v2.2 has been released on July 24, 2018.
New Plugin	ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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...

Ccp4 ncont

Overview

Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT. Usage of ccp4_ncont script in PyMOL allows easy selection of residues and atoms listed in ncont.log file. Interacting protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.

The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite (NCONT analyses contacts between subsets of atoms in a PDB file). First, we run NCONT on our pdb file to find interface residues. Then by using the ccp4_ncont script in PyMOL we separately select residues and atoms listed in a ncont.log file. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in NCONT log file.

This script works best for ..→

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.
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+|- 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
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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]]'')
-||'''[[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
+! POSF
-| 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 [https://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/].
+| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
-|-
-! 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
+! Tutorial
-| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
+| [[Plugins Tutorial]] updated for PyQt5
 |-
-! New Script
+! Official Release
-| [[DistancesRH|Distances RH]]
+| [https://pymol.org PyMOL v2.2 has been released] on July 24, 2018.
-|-
-! 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
-| 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
 |-
 ! New Plugin
-| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 |-
-! 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 58: @@
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Difference between revisions of "Main Page"

Revision as of 06:57, 27 November 2018

Ccp4 ncont

Overview

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