I would like to compare several very similar structures (more than 10) to get the rms deviation over all. Is this possible with any program?
Thanks
Katie Carr
University of Nottingham
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Eleanor Dodson
Sent: 14 April 2011 11:51
To: [log in to unmask]
Subject: Re: [ccp4bb] Comparing two proteins
On 04/13/2011 09:18 PM, REX PALMER wrote:
> Dear All
> What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions.
>
> Rex Palmer
> Birkbeck College
Using CCP4 go to the coordinate utility
Superpose molecules
You can either compare things using secondary structure or by specifying
residue spans
Underlying programs are PISA (also available at the BI msd server) and
LSQKAB
Eleanor
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