Hi Camille, ChimeraX does not move the proteins to predict how they might bind each other, although you could move one relative to the other "manually" (with the mouse) yourself, or use some other program to do protein-protein docking. ChimeraX is just showing the coordinates in the Protein DataBank data files that you opened, i.e. whatever the authors deposited.

If you are using ChimeraX, for future questions you may want to use ChimeraX mailing list chimerax-users@cgl.ucsf.edu CC'd here instead of the Chimera one.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 30, 2022, at 3:26 PM, Lake, Camille (NIH/NIAID) [C] via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Hello,

My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space.

Thank you,

Camille