Hi George, Thanks for catching this bug in the alphafold interfaces command. The code failed to pass the specified distance and max_pae parameters down to the key routine that computes the dimer confidences so that routine just used the default values. I've fixed it in the ChimeraX daily build and 1.10 release candidates that are made every night. Versions dated May 21, 2025 on the download page will have this fix. https://www.rbvi.ucsf.edu/chimerax/download.html Tom
On May 20, 2025, at 1:44 PM, George Belov via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Bruno and ChimeraX team, I apologize if I am addressing my request incorrectly, as this is the first time I am using this mailing list option. I would like to follow up on the functionality of the alphafold interface command: I ran the command with default parameters (distance <=4, PAE <=5), got the following results in the log
4 of 478 dimers have 10 or more confident residue interactions spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
they were recorded in the csv file as expected, with the headings of
distance max_pae 4 5
I run the command the second time with more relaxed parameters (or so I though) of the distance <=5 and PAE<=6, here is the log record of the command:
alphafold interfaces E:\2BC_and_LDs\AF_predictions\PDB_structures_true\Extracted_ALL distance 5 maxPae 6 resultsFile Interfaces_5_6.csv,
And got the following result record in the log:
4 of 478 dimers have 10 or more confident residue interactions spanning <= 5.0 Angstroms with predicted aligned error <= 6.0 Angstroms.
I.e. it seems that the command worked with the new parameters, but in fact the csv file again shows the headings of distance max_pae 4 5
and the results in the new file are identical to the previous run with the default parameters. I should mention that I removed the first csv result file from the directory before running the command the second time with new parameters.
Am I doing something wrong with providing the alphafold interface with new parameters? Thank you. George
On Tue, May 20, 2025 at 4:08 AM Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear Tom, Dear Elaine
Thanks for your thorough explanation.
I am working with 42 structures, all produced by the af3 server. The one I sent was an MRE.
@Tom: To sum up, 1. Those outputs summarise the interface properties in terms of contacts, and the most synthetic indicator of interface confidence/stability [1] is confident pairs. When contextualising this indicator, one should remember that since proximity can be many-to-one and confidence is based on PAE, the number of confident pairs cannot be related to the sum of residues involved from the two chains. Also, when using AF3 models, one should be sure not to have nonstandard residues and/or ligands and rely on the CSV.
[1] Maybe stability is too much...
P.S.: Regarding netiquette, should I also reply to your address or the mailing list?
-- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- ---------------------------------------- George A. Belov, Ph.D. Professor Department of Veterinary Medicine University of Maryland Va-Md College of Veterinary Medicine 8075 Greenmead Dr., room 1215 College Park, MD 20742 Phone: 301-314-1259 _______________________________________________ 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/