Enquires about predicting protein interaction with chimeraX/AlphaFold
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
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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, Thank you so much for your fast response. I just checked the documentation and I'm a little uncertain if I was understanding it correctly. May I ask if I want to predict a protein complex, all I need to do is to put a comma between the 2 sequence and if there is an interaction, the complex will be automatically predicted and there is nothing more I need to select? Again, thank you so much for your help. Best Wishes Yiling Lan ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 20, 2023 12:42 PM To: Yiling Lan <ylan03@syr.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Enquires about predicting protein interaction with chimeraX/AlphaFold 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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Yiling Lan, My understanding is that AlphaFold does not really predict whether or not there is a complex. Instead, when you submit 2 sequences (yes with comma between, as in the video and as it says in the help page), you are telling it to generate a complex. AlphaFold will try to generate a reasonable 3D structure for a complex because that was the task it was given. AlphaFold Predict help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> As to whether you need to do select anything or change other options, you can take default settings or you can decide to change them. We try to make the default settings reasonable, but you may want to look at the help for the options (in the link above) to decide whether they are what you want. 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 11:04 AM, Yiling Lan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thank you so much for your fast response. I just checked the documentation and I'm a little uncertain if I was understanding it correctly. May I ask if I want to predict a protein complex, all I need to do is to put a comma between the 2 sequence and if there is an interaction, the complex will be automatically predicted and there is nothing more I need to select? Again, thank you so much for your help. Best Wishes Yiling Lan
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 20, 2023 12:42 PM To: Yiling Lan <ylan03@syr.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Enquires about predicting protein interaction with chimeraX/AlphaFold
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@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>
Dear Elaine, Thank you so much for your response and invaluable help. Hope you have a great weekend. Best Wishes Yiling Lan ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 20, 2023 2:29 PM To: Yiling Lan <ylan03@syr.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Enquires about predicting protein interaction with chimeraX/AlphaFold Dear Yiling Lan, My understanding is that AlphaFold does not really predict whether or not there is a complex. Instead, when you submit 2 sequences (yes with comma between, as in the video and as it says in the help page), you are telling it to generate a complex. AlphaFold will try to generate a reasonable 3D structure for a complex because that was the task it was given. AlphaFold Predict help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> As to whether you need to do select anything or change other options, you can take default settings or you can decide to change them. We try to make the default settings reasonable, but you may want to look at the help for the options (in the link above) to decide whether they are what you want. 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 11:04 AM, Yiling Lan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thank you so much for your fast response. I just checked the documentation and I'm a little uncertain if I was understanding it correctly. May I ask if I want to predict a protein complex, all I need to do is to put a comma between the 2 sequence and if there is an interaction, the complex will be automatically predicted and there is nothing more I need to select? Again, thank you so much for your help. Best Wishes Yiling Lan
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 20, 2023 12:42 PM To: Yiling Lan <ylan03@syr.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Enquires about predicting protein interaction with chimeraX/AlphaFold
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@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>
participants (2)
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Elaine Meng -
Yiling Lan