| Wiki Update
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Wiki has been updated. Please report any problems to the sysops.
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| New Scripts
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Create objects for each molecule or chain in selection with split_object and split_chains
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| New Script
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Rotkit: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
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| New Script
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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.
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| New Script
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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.
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| New Script
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PluginDirectory: How to set up a personal plugin directory
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| New Script
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Add focal blur to images FocalBlur.
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| New Script
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Visualize VDW clashes with show bumps
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| New Plugin
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Color by DSSP or Stride secondary structure assignment
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| New Script
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There is a new script to calculate the Radius of gyration
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| New Command
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Map_set Performs a given operation on a map: can create consensus volumes, for example.
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| New Script
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ColorByDisplacement Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.
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| New Script
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DisplacementMap Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
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| New Script
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Two new scripts: AAindex and Sidechaincenters
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| New Plugin
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CAVER_2.0 update to the CAVER plugin.
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| New Script
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AngleBetweenHelices calculates the angle between two helices.
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| Search
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GoogleSearch widget fixed.
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| New Script
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Spectrumany creates color gradients with arbitrary color sequences.
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| New Script
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BbPlane will draw CGO planes across the backbone highlighting planarity of arrangement.
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| New Script
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Center Of Mass has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere).
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| New Script
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Jump is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
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| New Scripts
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ResDe is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
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| New Script
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See BiologicalUnit, for a workaround to the buggy Symexp command or if you just want to learn more about symmetry expansion in PyMOL.
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| New Script
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See Supercell, the new script for making XxYxZ supercells.
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| New Script
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See Split_Object_Along_Axis, for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
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| New Script
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See Consistent_View/_Map_Inspect, which is a toolkit for rapidly inspecting multiple maps and models.
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| Server updates
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The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend. We are now fully functional. A deep thanks to BitGnome for donating time and hardware for the PyMOL project.
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| fetch_host setting
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Fetch_Host has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
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| Fetch
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Fetch has been updated to also load electron density maps.
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| Schrodinger Buys PyMOL
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Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the sale.
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| User Movie
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One of our users has posted another interesting movie, images from which were created with PyMOL.
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| New setting
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surface_cavity_mode to change how PyMOL displays cavities.
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| Search fixed.
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Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
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| New Command
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Cache—stores information on structures, so we don't have to recompute them.
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| Warren
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News about Warren DeLano's passing may be read on Warren's memorial page.
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| Setting
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Fetch_Path—Sets the default path for the fetch command.
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| New Script
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SelInside—Creates a custom selection of all atoms spatially inside some user-defined box.
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