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.