Hello Hidhi, On Wed, 2014-07-23 16:39 EDT, Nidhi Jatana <nidhijat...@bic-svc.ac.in> wrote:
> Dear Sir/Madam > I have generated five models for a protein and I wanted to check how the > models align to each other and color them by RMSD/RMSF. I wanted to know > what should be the ideal way to do it. Shall I use RMSF or RMSD for the > same? You should use the RMSF calculation as that takes into account all of the structures. RMSD is a calculation that applies only to pairs of structures. > I tried doing this using rmsf_states.py and color_b.py scripts: As the author, I am somewhat familiar with these scripts. :) > - First I merged the five pdb files with load command, generating a > multi-state model > - Next, I used rmsf_states.py script to generate b-factors (using > command: rmsf_states tasser, byres=1, reference_state=1) > - Next I used the color_b.py script to color the structures (using > command: color_b(selection='all', item='b', mode='hist', > gradient='bgr') ) > > Is this the correct way to do it? It sounds correct to me. Did it not produce the result you expected? By setting byres=1, you are automatically only calculating the RMSF for the C-alpha atoms of each residue, but that value is then used to modify the B-values of all of the atoms in each residue. > And there is one more query. When I am loading the multi-state model, I > could only see one structure, not all five? Can I visualize all 5? Yes, as Andreas said to turn on the display of all states: set all_states, 1 and to revert to just showing a single state: set all_states, 0 Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds _______________________________________________ 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
