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Revision as of 03:58, 4 March 2019

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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
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 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...

Pseudoatom

pseudoatom creates a molecular object with a pseudoatom or adds a pseudoatom to a molecular object if the specified object already exists. Default position is in the middle of the viewing window.

USAGE

pseudoatom object [, selection [, name [, resn [, resi [, chain
        [, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
        [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]

ARGUMENTS

  • object = string: name of object to create or modify
  • selection = string: optional atom selection. If given, calculate position (pos) as center of this selection (like center of mass without atom masses).
  • name, resn, resi, chain, segi, elem, vdw, hetatm, b, q = string: atom properties of pseutoatom
  • color = string: color of pseudoatom
  • label = string: place a text label and hide all other representations
  • pos = 3-element tuple of floats: location in space (only if no selection given)
A Random PyMOL-generated Cover. See Covers.