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| | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates | | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates |
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| − | ! New Plugin | + | ! PyMOL Open-Source Fellowship |
| − | | [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL. | + | | Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship |
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| − | ! 3D using Geforce | + | ! Official Release |
| − | | PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ 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. | + | | [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015. |
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| | ! New Plugin | | ! New Plugin |
| − | | [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS. | + | | [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL. |
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| − | ! New Software
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| − | | [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
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| − | ! New Script
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| − | | [[cgo_arrow]] draws an arrow between two picked atoms.
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| − | ! Tips & Tricks
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| − | | Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
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| − | ! New Script
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| − | | [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
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| − | ! New Script
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| − | | [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
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| − | ! New Script
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| − | | [[DistancesRH|Distances RH]]
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| − | ! PyMOL on the iPad
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| − | | PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
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| − | ! OS X Compatibility
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| − | | Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
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| − | ! New Script
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| − | | [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
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| − | ! New Script
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| − | | [[b2transparency]] can set surface transparency based on atom b-factor
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| − | ! New Extension
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| − | | [[psico]] is a python module which extends PyMOL with many commands
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| − | ! New Script
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| − | | [[uniprot_features]] makes named selections for sequence annotations from uniprot
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| | ! New Plugin | | ! New Plugin |
| − | | [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein. | + | | [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds. |
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| − | ! New Script
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| − | | [[set_phipsi]] can set phi/psi angles for all residues in a selection
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| − | ! New Script
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| − | | [[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.
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| − | ! New Script
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| − | | [[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!
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| − | ! New Script
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| − | | [[cyspka]] is an experimental surface cysteine pKa predictor.
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| | ! New Plugin | | ! New Plugin |
| − | | [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]]. | + | | [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL. |
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| − | ! New Script | + | ! 3D using Geforce |
| − | | [[spectrum_states]] colors states of multi-state object
| + | | PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ 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. |
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| − | ! New Script
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| − | | [[TMalign]] is a wrapper for the TMalign program
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| − | ! Gallery Updates
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| − | | The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
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| − | ! New Script
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| − | | [[save_settings]] can dump all changed settings to a file
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| − | ! Tips & Tricks
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| − | | Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
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| − | ! 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 [http://propka.ki.ku.dk/ 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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| | ! Older News | | ! Older News |
