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News & Updates Official Release PyMOL v3.0 has been released on March 12, 2024. New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models 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 fellowship announced for 2022-2023 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... SelectClipped This script selects those atoms that are between the near and far clipping plane. Usage select_clipped [name [, selection [, state]]] The Code from pymol import cmd def clipped_by(at,v): x,y,z = at.coord nz = v[2]*(x-v[12])+v[5]*(y-v[13])+v[8]*(z-v[14])-v[11] return nz > v[15] and nz < v[16] def clipped(selection="all",state=1): v = cmd.get_view() return [ i.id for i in cmd.get_model(selection,state).atom if clipped_by(i,v) ] def select_clipped(name='clipped', selection='all', state=1): ''' DESCRIPTION Select atoms between clipping planes USAGE select_clipped [name [, selection [, state]]] ''' state = int(state) cmd.select(name, 'none') for model in cmd.get_object_list('(' + selection + ')'): cmd.select_list('__tmp', model, clipped('(%s) and (%s)' % (model, selection), state)) cmd.select(name, '__tmp', merge=1) cmd.delete('__tmp') cmd.extend('select_clipped', select_clipped) To use this script save it to ..→

A Random PyMOL-generated Cover. See Covers.