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

Re: [ccp4bb] relative domain motion calculation...

Dear Mintu, one possible option is the webserver 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

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" wrote: >Dear All, >I am working with a protein containing tandem domains, connected with >3-4 residue linker. I want to calculate th

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

[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%). P