Hi Sebastien, If you have multiple poses of the same molecule in your sdf file, you can translate them into a multi-model PDB file, writing the score and rmsd values to the bfactor and occupancy field. This you can then load into pymol, allowing you to step through the poses. With the command 'spectrum' you can colour according to b-factor or occupancy, allowing a quick judgment of the quality of a certain pose. I'm not sure if it will also work that way if the sdf file contains different molecules.
Hope it helps, Tsjerk On Mon, Aug 30, 2010 at 9:51 AM, Sebastian Kruggel <[email protected]> wrote: > dear all, > > i try to find a way of displaying data about molecules > contained in a sdf file (score and rmsd values of docked > poses) - at the best as labels. > > in the mailing list i only find information about displaying > the title or splitting the sdf. i would like to keep the > multimolecular character of the file (to go through the > poses) but display the data of the sdf. is there any way to > do this? > > thanks in advance, > sebastian > > > > > -- > Sebastian Kruggel > Institut für Pharmazie > Bundesstr. 45 | Raum 112 (406) > D 20146 Hamburg > > Tel: +49 (0)40 42838-3626 (-3484) > mail: [email protected] > http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html > > ------------------------------------------------------------------------------ > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program > Be part of this innovative community and reach millions of netbook users > worldwide. Take advantage of special opportunities to increase revenue and > speed time-to-market. Join now, and jumpstart your future. > http://p.sf.net/sfu/intel-atom-d2d > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands ------------------------------------------------------------------------------ Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
