[Chimera-users] Making oligomers from Alphafold predictions

[Tom Goddard]

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 at 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 at stanford.edu <mailto:kjude at stanford.edu>> wrote:
>  Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server
> 
> https://rosie.rosettacommons.org/symmetric_docking <https://rosie.rosettacommons.org/symmetric_docking>
> --
> 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
> Phone: (650) 723-6431 <tel:%28650%29%20723-6431>
> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users at cgl.ucsf.edu <mailto:chimera-users at 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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