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> 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
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