Hi Smith,

Do you know the symmetry of the oligomer you are trying to make?  Is it just a matter of applying positions that you already know?  Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)?  If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation).

tom


On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thank you, Elaine and Kevin, for your response. 
The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. 

Thank you. 

Best 
Smith

On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude@stanford.edu> wrote:
 Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server


--
Kevin Jude, PhD (he/him/his)
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305

On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi All,
Apologies for the nonrelated question!!

Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure.   Please let me know. I will be grateful for your kind responses. Thank you 

Best
Smith
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