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
