Dear Mintu,
If I understand your scenario correctly, you are referring to a single
structure where you want to get the relative inter-domain orientation
within the one protein.
So, after having watched the Chimera tutorial movie linked in the
previous answer (just out of curiosity) and then having tried that
myself, I would say that the process is simpler in your case than for
the example shown:
1. split your protein into two different models for the domains
2. MatchMaker
3. measure rotation #0 #1
By the way, if you are generally interested in domain matching and
domain movement between different conformers of a protein - that is,
usually from two (or sometimes more) distinct structures, you might want
to have a look at the RAPIDO web-service as well:
http://webapps.embl-hamburg.de/rapido
This might be a useful tool in particular when the "domains" in terms of
rigid parts of a structure are not obvious a priori.
Best regards,
Fabio
On 21. 04. 2015 09:39, Mintu Chandra wrote:
Dear All,
I am working with a protein containing tandem domains, connected with
3-4 residue linker. I want to calculate the relative
motion/orientation of one domain with respect to the hinge region as
well as with respect to the other domain. Both the domains have very
less seq. identity (<20%). Please suggest some web server to calculate
the same.
Thanks,
Mintu
--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
Notkestraße 85, Bldg. 25a
D-22607 Hamburg
phone: +49 (0)40 89902-178
fax: +49 (0)40 89902-149
e-mail:fabio.dallanto...@embl-hamburg.de
