This is a read-only mirror of pymolwiki.org

Main Page

From PyMOL Wiki
Revision as of 03:21, 22 June 2021 by Cchem (talk | contribs) (2 revisions)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search
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...

Pucker

Type Python Script
Download pucker.py
Author(s) Sean M. Law
License -
This code has been put under version control in the project Pymol-script-repo

DESCRIPTION

pucker.py is a PyMol script that returns the sugar pucker information (phase, amplitude, pucker) for a given selection.

This script uses its own dihedral calculation scheme rather than the get_dihedral command. Thus, it is lightning fast!

If a selection does not contain any ribose sugars then an error message is returned.

USAGE

load the script using the run command

pucker selection
#Calculates the sugar information for the given selection

pucker selection, state=1
#Calculates the sugar information for the given selection in state 1

pucker selection, state=0 
#Iterates over all states and calculates the sugar information for the given selection

EXAMPLES

<source lang="python">

  1. fetch 1BNA.pdb

fetch 1bna

  1. Select DNA only
  2. Otherwise, you will get an error for water not having sugars

select DNA, not solvent

  1. Execute pucker ..→
A Random PyMOL-generated Cover. See Covers.