Re: [ccp4bb] relative domain motion calculation
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
Re: [ccp4bb] relative domain motion calculation...
Dear Mintu, one possible option is the webserver DynDomhttp://fizz.cmp.uea.ac.uk/dyndom/. Kind regards, Matic 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 attachment: matic_kisovec.vcf
Re: [ccp4bb] relative domain motion calculation...
I am not sure about a web server, but if you use gesant to align one domain of the two structures, then fit the second domain of structure 1 to the second domain of the aligned structure 2; the polar angle Kappa will give you the amount of rotation between the second domains. Eleanor On 21 April 2015 at 08:39, Mintu Chandra mi...@iiserb.ac.in 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
[ccp4bb] relative domain motion calculation...
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
Re: [ccp4bb] relative domain motion calculation...
Hi Mintu You can use Chimera to calculate rotation angel. http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/ Veerendra On 21/4/15 3:39 PM, Mintu Chandra mi...@iiserb.ac.in 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 Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.
