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.
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