[PyMOL] Fwd: color by RMSF or RMSD

[Nidhi J. <nid...@bi...>]

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?

I tried doing this using rmsf_states.py and color_b.py 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?

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?


Thanking you

Regards

-- 
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.