Re: [PyMOL] bond connection file
Hi Vishwas, atom connectivity is the same for all states unless you have a discrete object. Try this: PyMOL set connect_mode, 1 PyMOL load file.pdb, discrete=1 Cheers, Thomas Vishwas Vasisht wrote, On 10/05/12 08:59: Hi Thomas, Thanks, it works for single frame. But when I use multiple frame (using MODEL and ENDMDL), the connections which i specified in the first frame is retained for rest of the frames. Am I doing some mistake in the way I wrote my PDB file? Regards Vishwas 2012/10/4 Thomas Holder spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote, On 10/04/12 16:52: Hi, I want to feed in a coordinates of atoms along with bond connection information. Since the bonding is based on some calculation I do, I need to include this information by hand. I tried to output the trajectory from my analysis in .mol format (following some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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] bond connection file
Does every MODEL ENDMDL have a unique Connection list? Can you show me your PDB file? Jordan On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht vishwas.vasi...@gmail.com wrote: Hi Thomas, Thanks, it works for single frame. But when I use multiple frame (using MODEL and ENDMDL), the connections which i specified in the first frame is retained for rest of the frames. Am I doing some mistake in the way I wrote my PDB file? Regards Vishwas 2012/10/4 Thomas Holder spel...@users.sourceforge.net Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote, On 10/04/12 16:52: Hi, I want to feed in a coordinates of atoms along with bond connection information. Since the bonding is based on some calculation I do, I need to include this information by hand. I tried to output the trajectory from my analysis in .mol format (following some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Whoever fights monsters should see to it that in the process he does not become a monster. And when you look into an abyss, the abyss also looks into you. -- Friedrich Nietzsche -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev___ 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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev___ 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] bond connection file
Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote, On 10/04/12 16:52: Hi, I want to feed in a coordinates of atoms along with bond connection information. Since the bonding is based on some calculation I do, I need to include this information by hand. I tried to output the trajectory from my analysis in .mol format (following some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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
