[Chimera-users] Making oligomers from Alphafold predictions

[Tom Goddard]

Hi Tiru,

If the center of symmetry is at 0,0,0 for your model and it just needs 6 rotated copies placed use Chimera command

	sym #0 group c6

where #0 is the model number of your monomer.  If you do not know the center of symmetry or how the monomers interface with each other (ie their orientation in the hexamer), then that is a protein-protein docking problem and the sym command does not solve that.  For that case you would need to fit in a cryoEM or X-ray map of the hexamer, or align the monomer to a known homologous hexamer, or find some amazing oligomeric structure prediction tool.

	Tom




> On Sep 1, 2021, at 11:24 AM, Tiru Hcu <tiru.hcu09 at gmail.com <mailto:tiru.hcu09 at gmail.com>> wrote:
> 
> Hi Tom, 
> 
> Thank you for your response. My protein symmetry is a hexamer. Please would you mind sharing a little elaborate how to to do in chimera. Thank you. 
> 
> Best regards,
> Tiru
> 
> On Wed, 1 Sep 2021, 21:10 Tom Goddard via Chimera-users, <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
> 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 <mailto: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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