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News & Updates
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Official Release PyMOL v2.1 has been released on March 13, 2018.
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
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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...


selInside selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples.


# find all atoms inside the box spanned by (0,0,0) and (10,10,10)
# for the example PDB, 1hpv
fetch 1hpv
pseudoatom b1, pos=[0,0,0]
pseudoatom b2, pos=[10,10,10]
selInside b1 or b2

The Code

<source lang="python"> import pymol from pymol import cmd, stored from random import randint

def selInside(bounding_object, target="*", radius=None):

   Selects all atoms of a given target type inside some selection that acts like a bounding box.
       bounding_object -- [PyMOL object/selection] the object/selection inside of which we want to choose atoms
       target -- [PyMOL selection] that defines the atoms to select.  Use "solvent" to select
                 only solvent atoms inside the selection
       radius -- [float] expand the box by this many angstroms on all sides
       (string) name of the selection created
A Random PyMOL-generated Cover. See Covers.