Hi Sasi, > I would like to read a CHARMM generated dcd file which has 200 frames in > it.
PyMOL can read DCD files with the "load_traj" command if it has been compiled with VMD plugins enabled. http://pymolwiki.org/index.php/Load_Traj An alternative python only implementation is available with the "psico" module as "load_traj_dcd" (http://pymolwiki.org/index.php/Psico). > Is there a way where I can upload dcd and know the rmsd of each > residue in the protein over 200 frames. Calculating RMSD for each residue separatly is possible, but requires some scripting. You need the "rms_cur" command for that. http://pymolwiki.org/index.php/Rms_cur > What do I have to do to switch off the graphics to speed up the process. You can run PyMOL in "batch mode" with "pymol -cr script.py". > I would appreciate if someone could take some time out to explain the > steps I should do to read a dcd file and find out the RMSD of the > residues of the protein only. For a protein with 100 residues, the script should look similar to this: python cmd.load('topology.pdb', 'mol') cmd.load_traj_dcd('trajectory.dcd', 'mol', 1) for state in range(1, cmd.count_states()+1): for resi in range(2, 100): sele = 'resi %d' % (resi) rmsd = cmd.rms_cur(sele, sele, 1, state) print 'State=%d Residue=%d RMSD=%f' % (state, resi, rmsd) python end Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
