From: Martin H. <mar...@gm...> - 2008-05-28 09:21:02
Attachments:
loadGroNdx.py
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Hi all, here's a small script that allows loading of a gromacs index file into pymol. The corresponding molecule has to be loaded with preserved atom order. I have also a question/feature request concerning the "load" operation: Is it possible to register e.g. this script, to handle loading of .ndx files. This would in particular be nice to load .gro files with a small script calling editconf -f toload.gro -o /tmp/loadme.pdb and then loading the pdb. Did I miss that option or doesn't it exist (at the moment)? Best Martin |
From: Tsjerk W. <ts...@gm...> - 2008-05-28 12:25:54
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Hi Martin, Now why didn't I ever think of that? So simple... In the .pymolrc you can add: import os /def gro( fnm ):\ os.system("editconf -f %s -o /tmp/tmp.pdb" % fnm )\ cmd.load( "/tmp/tmp.pdb", fnm[:-4] ) cmd.extend( "gro", gro ) And it will do what you want... Cheers, Tsjerk On Wed, May 28, 2008 at 11:21 AM, Martin Höfling <mar...@gm...> wrote: > Hi all, > > here's a small script that allows loading of a gromacs index file into pymol. > The corresponding molecule has to be loaded with preserved atom order. > > I have also a question/feature request concerning the "load" operation: Is it > possible to register e.g. this script, to handle loading of .ndx files. This > would in particular be nice to load .gro files with a small script calling > editconf -f toload.gro -o /tmp/loadme.pdb and then loading the pdb. > > Did I miss that option or doesn't it exist (at the moment)? > > Best > Martin > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |