[Chimera-users] AlphaFold Modeling

[Elaine Meng]

Hi Raihan,
If you are using Chimera, it does not have AlphaFold prediction.  Chimera has Modeller comparative modeling (based on template structure) with default number of models = 5, but you can change that in the "Advanced Options" on the Modeller comparative modeling tool: in that section, juist change the "Number of output models" value.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>

If you are using ChimeraX, it has both Modeller Comparative Modeling, and AlphaFold prediction.  However, the Alphafold prediction only gives you one model.   If you are using ChimeraX, it is better to send your question to the address chimerax-users at cgl.ucsf.edu ... either way please be clear about which program and which tool you are using.  Thanks!

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 31, 2022, at 1:09 PM, S.M. RAIHAN RAHMAN via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi!
> Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models? Please let me know. Thank you.
> 
> Regards,
> Raihan