Hi Suhaila, >From what I understand from the wiki, you have to have a match between the PDB and the contact map. If your contact map was made on a structure with multiple chains, all chains will be in there. If you want to select a single chain, you have to extract that chain from thhe PDB file, then run g_mdmat, and then load the PDB file and the map into Pymol.
Hope it helps, Tsjerk On Mon, Mar 12, 2012 at 1:43 PM, Suhaila Haji Mohd Hussin <bell_beaut...@hotmail.com> wrote: > Hello guys, > > Regarding the subject mentioned above, I'm wondering if PDB file has more > than one chain, will the generation of contact map using g_mdmat from > Gromacs > still produce a map of all chains? > > Don't I have a choice to choose one chain? > > Refer the subject above for more details: > http://www.pymolwiki.org/index.php/Contact_map_visualizer > > Cheers, > Suhaila. > > ------------------------------------------------------------------------------ > 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 (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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ 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 (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
