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News & Updates 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. New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS. New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL. New Script cgo_arrow draws an arrow between two picked atoms. Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL. New Script Cluster Count calculates statistics on the B-values for all atoms in the selected object. New Script Make Figures aids you in making publication quality figures for the currently displayed scene. New Script Distances RH PyMOL on the iPad PyMOL is now available on the iPad as a free download from the AppStore. See pymol.org/mobile for more info. OS X Compatibility Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here X11 Libraries. 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. See CMPyMOL. 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... Set name set_name can be used to change the name of an object or selection. Not only can you simply rename an object or selection, but this command is also a powerful tool for those who deal with multiple structures in one file --- say a collection of NMR models. The user can execute the Split_States command and then rename the molecule of choice in the state of choice. For example, if one loads an NMR structure (with, say, 20 states) and aligns it to another structure, the balance of the alignment will (most likely) be off due to the weighting of the 19 other structures you probably don't see. To overcome this problem, one simply executes Split_States and then renames one of the states and then aligns that newly renamed object. USAGE set_name old_name, new_name PYMOL API cmd.set_name(string old_name, string new_name) User Comments/Examples cmd.set_name("example", "nicename") As the order of arguments is different from, for example, the ..→

A Random PyMOL-generated Cover. See Covers.