Hello I have a commercial license of ChimeraX, I have a question you may be able to help with I have used Structure prediction > Alphafold to predict structures and interactions between 2 proteins and this returned the best_model.pdb But I would like to identify contacts within 8 angstroms, as shown in the Youtube video: https://www.youtube.com/watch?v=TMcjEecFHaI&list=WL&index=26'm typing the command: alphafold contacts /A to /B distance 8 But receive the error: 'Structure best_model.pdb #1 does not have PAE data opened' Do I need to open something? If you can help that would be much appreciated Many thanks Tony Anthony Newcombe PhD Applied Biopharm Consulting Ltd Cork, Ireland http://www.appliedbiopharm.com<http://www.appliedbiopharm.com/> IE: +353 (0)87 3634486 [cid:image001.png@01DBD2E1.AD97E890] Applied Biopharm Consulting Limited is a company located in the Republic of Ireland Reg. No: 747251, VAT No: IE4188817RH. Registered office: Brook Lodge, Lisnacunna, Ballinascarthy, Clonakilty, Cork, Ireland P85 C832. This message is confidential and intended solely for the recipient(s). If you are not the intended recipient, any use, disclosure, copying or distribution of this message or its attachments is strictly prohibited. Please notify the sender immediately by replying to this email and delete the message, its attachments and any copies.
Hi Tony, You need to open the PAE associated to your best model. Go to Tools/Structure Prediction/Alphafold Error Plot and select the folder containing your PAE 🙂 Celine _________________________________ Celine Bouchoux Principal Laboratory Research Scientist The Francis Crick Institute Uhlmann's Lab 1 Midland Road London NW1 1AT T: +442037961773 E: celine.bouchoux@crick.ac.uk<mailto:email%20address@crick.ac.uk> W: www.crick.ac.uk<http://www.crick.ac.uk> ________________________________ From: Anthony Newcombe via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 01 June 2025 10:41 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] ChimeraX support: Alphafold contacts External Sender: Use caution. Hello I have a commercial license of ChimeraX, I have a question you may be able to help with I have used Structure prediction > Alphafold to predict structures and interactions between 2 proteins and this returned the best_model.pdb But I would like to identify contacts within 8 angstroms, as shown in the Youtube video: https://www.youtube.com/watch?v=TMcjEecFHaI&list=WL&index=26 I’m typing the command: alphafold contacts /A to /B distance 8 But receive the error: ‘Structure best_model.pdb #1 does not have PAE data opened’ Do I need to open something? If you can help that would be much appreciated Many thanks Tony Anthony Newcombe PhD Applied Biopharm Consulting Ltd Cork, Ireland www.appliedbiopharm.com<http://www.appliedbiopharm.com/> IE: +353 (0)87 3634486 [cid:image001.png@01DBD2E1.AD97E890] Applied Biopharm Consulting Limited is a company located in the Republic of Ireland Reg. No: 747251, VAT No: IE4188817RH. Registered office: Brook Lodge, Lisnacunna, Ballinascarthy, Clonakilty, Cork, Ireland P85 C832. This message is confidential and intended solely for the recipient(s). If you are not the intended recipient, any use, disclosure, copying or distribution of this message or its attachments is strictly prohibited. Please notify the sender immediately by replying to this email and delete the message, its attachments and any copies. The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
Hi Tony, If you used ChimeraX's AlphaFold predict, there should be a results directory (click Options button on AlphaFold tool to see default location) including both your PDB files and associated other outputs including those with the PAE values. I don't have such results handy but they would probably be named similarly to the PDB files except ending in .json or .npy and you could try opening them with the "open" command, as mentioned briefly here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> My faint memory was that if you used Alphafold predict in ChimeraX it would automatically "know" which PAE goes with the structures that are automatically opened when the prediction is done, but maybe that is not the case. I hope this helps, 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 Jun 1, 2025, at 2:41 AM, Anthony Newcombe via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello I have a commercial license of ChimeraX, I have a question you may be able to help with I have used Structure prediction > Alphafold to predict structures and interactions between 2 proteins and this returned the best_model.pdb But I would like to identify contacts within 8 angstroms, as shown in the Youtube video: https://www.youtube.com/watch?v=TMcjEecFHaI&list=WL&index=26 I’m typing the command: alphafold contacts /A to /B distance 8 But receive the error: ‘Structure best_model.pdb #1 does not have PAE data opened’ Do I need to open something? If you can help that would be much appreciated Many thanks
Tony Anthony Newcombe PhD Applied Biopharm Consulting Ltd Cork, Ireland www.appliedbiopharm.com IE: +353 (0)87 3634486<image001.png>
Applied Biopharm Consulting Limited is a company located in the Republic of Ireland Reg. No: 747251, VAT No: IE4188817RH. Registered office: Brook Lodge, Lisnacunna, Ballinascarthy, Clonakilty, Cork, Ireland P85 C832. This message is confidential and intended solely for the recipient(s). If you are not the intended recipient, any use, disclosure, copying or distribution of this message or its attachments is strictly prohibited. Please notify the sender immediately by replying to this email and delete the message, its attachments and any copies. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Anthony Newcombe -
Celine Bouchoux -
Elaine Meng