to close the wizard, you can also apply
cmd.set_wizard("done")and you need to be carefull about the rotamer you're choosing. it happens that the first one ends up being in physically non-reasonable contact distance to other residues, so atoms become overlayed. also, the mutagenesis wizard has the funny habit of sometimes not adding hydrogens to terminal -C or -N after mutating a residue, just for the record.
Martin On 22.08.11 13:23, Troels Emtekær Linnet wrote:
Absolutely fantastic! :-) I got this to work with the pymol propka script. fetch 1ohr, async=0 create 1ohrB3C, 1ohr hide everything, all show cartoon, 1ohrB3C cmd.wizard("mutagenesis") cmd.do("refresh_wizard") # To get an overview over the wizard API: #for i in dir(cmd.get_wizard()): print i # lets mutate chain B residue 3 to CYS. (1ohrB3C) cmd.get_wizard().set_mode("CYS") cmd.get_wizard().do_select("/1ohrB3C//B/3") # Select the first rotamer, which is most probable cmd.frame(1) # Apply the mutation cmd.get_wizard().apply() # Close wiard cmd.wizard(None) # Find the new pka value import propka propka Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE<http://maps.google.dk/> 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/22 Martin Hediger <ma....@bluewin.ch <mailto:ma....@bluewin.ch>> Hi Troels It's indeed possible. The wizards are available through the cmd module. # Initialize load yourProtein cmd.wizard("mutagenesis") cmd.do("refresh_wizard") # To get an overview over the wizard API: for i in dir(cmd.get_wizard(): print i # lets mutate residue 104 to GLN cmd.get_wizard().set_mode("GLN") cmd.get_wizard().do_select("104/") # Select the rotamer cmd.frame(11) # Apply the mutation cmd.get_wizard().apply() There is alot more you could do inbetween these lines, but this is what I use it like. Martin On 21.08.11 15:56, Troels Emtekær Linnet wrote:Hi. I wonder if it is possible to interact with the mutagenesis wizard from the command line? I am trying to determine best mutants for FRET labelling, by predicting the pka value/reactivity for a possible cysteine. I would like to make a script that loops over the residues in my protein, change the residue to a cysteine, save the molecule and then initiate propka <http://pymolwiki.org/index.php/Propka> to get the pka for the cysteine. I have googled myself to: fetch 4ins, async=0 wizard mutagenesis cmd.get_wizard().do_select("/4ins//A/ASN`18/CB") cmd.get_wizard().do_pick("/4ins//A/ASN`18/CB") But I get: Error: please select an atom, not a bond. Can someone help here? Best Troels ------------------------------------------------------------------------------ Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it.http://p.sf.net/sfu/wandisco-d2d-2 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net <mailto:PyMOL-users@lists.sourceforge.net>) Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:http://www.mail-archive.com/pymol-users@lists.sourceforge.net------------------------------------------------------------------------------ uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net <mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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