[chimerax-users] Enquires about predicting protein interaction with chimeraX/AlphaFold

[Elaine Meng]

Dear Yiling Lan,
The video is older.  In the newer versions of ChimeraX, the AlphaFold tool does not have this option (it was removed), so you don't have to worry about it.  I would recommend using the newer versions of ChimeraX because there is a continuous improvement process.  Also, the older versions may not work any more because AlphaFold or ColabFold itself has also changed during this time.

The current (new) documentation for the AlphaFold tool is here:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>

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

> On Apr 20, 2023, at 10:11 AM, Yiling Lan via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX Developers,
> 
> Hope this email finds you well.
> I'm currently trying to predict the interaction of 2 proteins after watching the videos on youtube (Running AlphaFold to Predict Protein Complexes from ChimeraX). after installing the CimeraX (UCSF ChimeraX version: 1.6rc202304140213 (2023-04-14) version) but I did not see the check box for "Is prokaryotes? used for predicting complex). 
> May I ask if in newer version the check box for complex prediction is at somewhere else? If it does not bother too much, could you please let me know if there is anyway I can run complex prediction on 1.6rc?
> Thank you so much.
> Best Wishes
> Yiling Lan
> <Screenshot 2023-04-20 at 1.05.48 PM.png>_______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users