You mean something like changing the elbow angle between the domains and further exploring how it affects packing of the oligomer? Something like this would be relatively simple task in CNS, doing the rigid body minimization without experimental terms and with fake NOE restraints to force a certain elbow angle (or simply defining an additional restraint for however defined elbow angle. You can then follow up with simulated annealing to relax the linker region. All of this assumes, of course, that you are trying to come up with some way to determine what elbow angle range is permitted by your protein (without doing the full blown md simulation). If, on the contrary, you simply want to get few models with different orientation of subunits, disregarding their feasibility, then your best approach is to figure out the rotation axes for the elbow angle and then apply the corresponding set of transformations. Cheers, Ed. On Wed, 2011-02-09 at 14:57 -0500, Tatyana Sysoeva wrote:
Dear all,
I am working with a protein which form homooligomeric assembly. Each subunit of the assembly consists of 2 subdomains. I would like to create chimeras with the subdomains moved with respect to each other, keeping the linkers.
I am wondering what would be the easiest way to do this?
Any suggestions are welcome!
Sincerely, Tanya _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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