On Apr 4, 2022, at 11:32 PM, SANTOSH RAMA BHADRA RAO TATA <19807877@students.latrobe.edu.au> wrote:
Good evening, Meng,
I'm trying to bind to protein subunits A and B with the stoichiometry of A-A-B-A-B pentameric form how can I do that in chimera? I have both A and B PDB files single chains.
Thanking you,
With best wishes, Tata Santosh Rama Bhadra Rao, PhD Scholar, C/O Prof Helen Irving, La Trobe university, Bendigo, Vic-3550, Australia. Email: 19807877@students.latrobe.edu.au; S.Tata@latrobe.edu.au Phone: 0499263974
Hello, The recommended address for Chimera questions is chimera-users@cgl.ucsf.edu CC'd here. Chimera doesn't predict how A and B would bind each other. Instead you have to use any other information you might have. If there is a similar structure already known in pentameric form, then you could: - open the known pentamer - open the A structure 3 times and the B structure 2 times - superimpose each of your structures on one monomer of the known pentamer, e.g. with matchmaker See matchmaker (GUI tool or command) and other methods for superimposing structures: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco