Dear Fei, I think you might do that in Chimera, but it will be merely illustrative because you don't know the correct orientation of the proteins into the complex. I think you should go first for protein-protein docking program to predict the orientations of the proteins into the complex. Moreover, you can filter the docking predictions by keeping those that are according to your experimental results and then, visualize the predicted complexes in Chimera. For example, you can try with ClusPro server: http://cluspro.bu.edu/login.php Best, Aldo 2014-03-02 15:08 GMT-05:00 <fei.wu@chem.utah.edu>:
Dear Chimera Team,
I am studying the interactions between three enzymes with their biological assembly structures available in PDB. Using mass spectrometry, I have been able to identify interfacial residues, and what I want to do is build up a super complex (made of the three proteins) in a desired way that these proteins are oriented by interactions between experimentally-determined residues. Would you please tell me that, if I can make or draw this in chimera? And I am also trying to compare experimentally-proposed complex structure with simulated structure. Is there a specific way in chimera to simulate interactions between two or more proteins? I found that when I opened multiple protein files in one session, chimera would gave me a complex of these proteins (not always true with different pdb files). Is this an automatic generation of simulated protein complexes or just a superimposition of part of proteins?
Thanks, Fei
-- Fei Wu, Ph.D. candidate Shelley D. Minteer Group Chemistry Department University of Utah Phone: 385-234-0603 Email: fei.wu@chem.utah.edu _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- ========================================= Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera@cchmc.org <asegurac@ipn.mx>; aldosegura@gmail.com =========================================