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Select_sites News & Updates 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. New Script set_phipsi can set phi/psi angles for all residues in a selection New Script 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. 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! New Script cyspka is an experimental surface cysteine pKa predictor. New Plugin Contact_Map_Visualizer visualize residues corresponding to the contact map New Script spectrum_states colors states of multi-state object New Script TMalign is a wrapper for the TMalign program Gallery Updates The 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 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 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 See Older News.

Did you know... SelInside selInside selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples. Usage # 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 ..→

A Random PyMOL-generated Cover. See Covers.