Re: [PyMOL] Fwd: color by RMSF or RMSD

Hej Nidhi,

I'm not familiar with the two scipts but the usage appears correct. You can
check the arguments in PyMOL using e.g.:
rmsf_states ?
and/or:
help rmsf_states

I assume the color_b command is a simplification of the spectrum command,
so you could also check out:
http://www.pymolwiki.org/index.php/Spectrum

If you want to display several states, you can set 'all_states' to on:
set all_states, 1 # shows all states
http://www.pymolwiki.org/index.php/All_states

Alternatively, consider splitting the object states after you're done with
them:
http://www.pymolwiki.org/index.php/Split_states

Hope this helps out.

Cheers,

Andreas





On Wed, Jul 23, 2014 at 1:09 PM, Nidhi Jatana <nid...@bi...>
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?
>
> 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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