There are several AlphaFold-related videos in our video tutorials list, scroll down to near the bottom:
<
https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/videos/__;!!G92We9drHetJ8EofZw!aGYvVl8lZl1Nzln0bQc1LRXAuy-eZhUJdzUZWZb77amv_fxFlC6LDTfNRLneQsw8ku-B9lyD1ZkuyCreqTo$ >
Regards,
Elaine
> On Mar 16, 2026, at 9:52 AM, Ehsaneh Khodadadi via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
>
> Dear Dr. Meng
> Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help.
> If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet.
> Thank you again for your guidance.
> Best regards,
> EhsanehFrom: Elaine Meng <
meng@cgl.ucsf.edu>
> Sent: Monday, March 16, 2026 9:43 AM
> To: Ehsaneh Khodadadi <
ehsaneh@stanford.edu>
> Cc:
chimera-users@cgl.ucsf.edu <
chimera-users@cgl.ucsf.edu>; chimerax-users <
chimerax-users@cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX
> Dear Ehsan,
> Next time you may want to use the address for ChimeraX,
chimerax-users@cgl.ucsf.edu<
mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list.
>
> You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc.
>
> Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help:
> <
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html*predict__;Iw!!G92We9drHetJ8EofZw!aopAjIPFojbarRLl8WbVzLrG7ZmbaXssuxjamEAZ4finJaqGU6viwUA6jtf1z-Oz-bD_UOcYjACLFpRLSwI$ >
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
>
> > On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
> >
> > Dear ChimeraX Team
> > I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper.
> > I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction.
> > Could you please advise if there are specific settings or steps that might affect the prediction results?
> > Thank you very much for your help.
> > Best regards,
> > Ehsan Khodadadi
> >
> > _______________________________________________
> > Chimera-users mailing list --
chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to
chimera-users-leave@cgl.ucsf.edu> > Archives:
https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/__;!!G92We9drHetJ8EofZw!aopAjIPFojbarRLl8WbVzLrG7ZmbaXssuxjamEAZ4finJaqGU6viwUA6jtf1z-Oz-bD_UOcYjACL-zSFmgg$>
>
> _______________________________________________
> Chimera-users mailing list --
chimera-users@cgl.ucsf.edu> To unsubscribe send an email to
chimera-users-leave@cgl.ucsf.edu> Archives:
https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/__;!!G92We9drHetJ8EofZw!aGYvVl8lZl1Nzln0bQc1LRXAuy-eZhUJdzUZWZb77amv_fxFlC6LDTfNRLneQsw8ku-B9lyD1ZkuZzjUB2c$