[PyMOL] Query on Contact Map Visualizer
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
Re: [PyMOL] Query on Contact Map Visualizer
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
[PyMOL] How to tell what amino acids are in view?
Hi, Does anyone know of a way to tell which amino acids are currently in view? I am imagining something that highlights the the parts of the sequence that are visible as you rotate the molecule around. It may be much more complex than I am describing. Shane -- 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
Re: [PyMOL] How to tell what amino acids are in view?
Shane, The simplistic option is to use the shift key and drag your mouse across the viewer window. With the sequence displayed this will select those residues in view and highlight them also. This is the static option and I'm guessing not quite what you may be after Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -- 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
