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Re: [PyMOL] Display electrostatic potential at different pH
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From: Troels E. L. <tl...@gm...> - 2012-02-04 13:23:11
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How about using the APBS plugin? http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol The plugin that is shipped with Pymol as standard http://www.pymolwiki.org/index.php/APBS The same plugin, but in the Pymol-script-repo<http://www.pymolwiki.org/index.php/Git_intro> . Here the plugin is setup to find the included (psize.py) and (pdb2pqr.py) http://www.pymolwiki.org/index.php/Apbsplugin And calculate the PQR at different pH? http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr Server http://kryptonite.nbcr.net/pdb2pqr/ In the "Main" tab, in the APBS pymol plugin. Select: "Choose Externally generated PQR". Or use this: python pdb2pqr.py --ff=AMBER --with-ph=5 As far as I know, pdb2pqr, uses PROPKA 1.0 to get the pKa. There has been a large development to PROPKA since then. Version 3.1 is available at homepage: http://propka.ki.ku.dk/ If you want to visualize the pKa, try this Pymol script. http://www.pymolwiki.org/index.php/Propka Troels Emtekær Linnet Lyongade 24. 4.mf, 2300 København S Mobil: +45 60210234 2012/2/3 Xiaoshan Min <xs...@ya...> > Hi Pymoler, > > I want to present a structure to non-structural biologist. They want to > visualize the change of surface charge at different pH. For example, > Histidine will have different protonation state at pH 7.5 and 5. What > would be the best way to visualize this? I know an accurate calculation > probably is too hard, but would like to know if there is a clever way of > approximation. > > Thanks a lot. > > Xiaoshan > > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |