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Re: [PyMOL] list of polar contacts
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From: Jason V. <jas...@sc...> - 2012-01-31 16:04:00
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Hi Abhinav, The underlying C-object for a measurement does not support iterate/alter. This is rather silly; PyMOL should be able to tell you what's in the object. Please file a feature request on the open-source bug tracker and we'll be sure to look at this ASAP. Cheers, -- Jason On Tue, Jan 31, 2012 at 9:02 AM, Abhinav Verma <abh...@gm...> wrote: > Hi thanks, > > still it is not the same.. But thanks.. > I wish Jason can reply if there is any way to get the list from the apply > command. > > thanks, > Abhi > > On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis <te...@gm...> > wrote: >> >> I think you can reproduce the results from "apply->find->polar contacts" >> option with the PyMOL built-in "distance" command. E.g. >> >> distance hbonds, all, all, 3.2, mode=2 >> >> >> >> The problem is that you cannot set the A-H-D angle which is important for >> the definition of the H-bond. >> >> >> >> On 30 January 2012 18:45, Abhinav Verma <abh...@gm...> wrote: >>> >>> Thanks Thomas, >>> >>> I have been here and my problem is that I could not reproduce the >>> results of default pymol behaviour. I just need to either reproduce 100% the >>> pymol default behaviour or to just get a list of what is painted in the >>> window. It should be possible I guess. >>> >>> Do you have more ideas? >>> >>> >>> >>> >>> On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis <te...@gm...> >>> wrote: >>>> >>>> Probably because they set diffently the acceptor-donor cutoff and the >>>> acceptor-hydrogen-donor angle. Use list_hbonds.py from: >>>> >>>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ >>>> >>>> and set the cutoff and angle to the values you wish. >>>> >>>> Thomas >>>> >>>> >>>> >>>> On 30 January 2012 16:34, Abhinav Verma <abh...@gm...> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I am trying to get the list of hbonds formed using >>>>> Apply-find-polarcontacts. >>>>> >>>>> I searched and found some scripts, but they never give me the same >>>>> result as the one by default pymol. >>>>> >>>>> Any ideas how I can get the hbonds as a list. >>>>> >>>>> Thanks, >>>>> >>>>> Abhinav >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> 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... >>>> >>>> >>>> >>>> >>>> -- >>>> >>>> ====================================================================== >>>> >>>> Thomas Evangelidis >>>> >>>> PhD student >>>> >>>> Biomedical Research Foundation, Academy of Athens >>>> >>>> 4 Soranou Ephessiou , 115 27 Athens, Greece >>>> >>>> email: te...@bi... >>>> >>>> te...@gm... >>>> >>>> >>>> website: https://sites.google.com/site/thomasevangelidishomepage/ >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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... >>> >>> >> >> >> >> -- >> >> ====================================================================== >> >> Thomas Evangelidis >> >> PhD student >> >> Biomedical Research Foundation, Academy of Athens >> >> 4 Soranou Ephessiou , 115 27 Athens, Greece >> >> email: te...@bi... >> >> te...@gm... >> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> >> >> > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > 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-d2d > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
