Hi Bruno, Here are some explanations to help you understand the numbers. First if it says 23 confident pairs between 12 residues in one chain and 12 residues in the other chain it means just what it says. There are 23 pairs of residues which are which have atoms within 4A and PAE <= 5A. There are 12 residues in one chain that are in proximity to 12 in another. How many pairs are in proximity? You can't tell unless you inspect the structure since one residue in chain A may be near 3 residues in chain B, or near 5 residues in chain B or near 1 residue in chain B. So of course the number of confident pairs has no relation to the sum of the two sets of residues involved from the 2 chains. Interface residues are simply ones that meet the distance requirement to being within 4A of a residue in another chain. Confident residue pairs also have PAE <= 5. So of course the number of interface residues that are involved in confident pairs are a subset of the interface residues, and in many cases will be a much smaller number of residues than the total number of interface residues. The one question you raise that is a bit trickier is why alphafold interfaces and alphafold contacts report different numbers of confident pairs. There are two factors. The main one is that interfaces considers the minimum PAE from res1 to res2 and from res2 to res1, while alphafold contacts only considers pae from res1 to res2 (ie it is asymmetrical, alphafold contacts #1/A to #1/B gives different result than alphafold contacts #1/B to #1/A). The PAE values are not a symmetric matrix, the value from res1 to res2 is different than res2 to res1. If you don't understand why study the definition of PAE. So interfaces and contacts will give different results because one symmetrizes the PAE (using the minimum of the 2 values) while the other does not. A second reason why there are differences is that interfaces was developed to work with ColabFold, ie AlphaFold 2 which uses specific file names that contain parts "rank_1", "rank_2".... AlphaFold 3 doesn't have "rank" in th! e file name and so the interfaces code does not know the rank order. So when it Logs the table of results it is not necessarily giving the results for the highest rank prediction. Another pitfall of trying to use alphafold interfaces on AF3 results that it was not designed for is that AF2 only had PAE for residues, while AF3 also has PAE values for individual atoms for ligands and non-standard residues. If there are atom PAE values then the alphafold interfaces command will give completely wrong results since it was written before AF3 came out and only knows about AF2 per-residue PAE. It looks to me that the AF3 prediction you attached has only per-residue PAE so the results are meaningful and interfaces.csv contains the values for all of the 5 predictions so you can sort out the rank problem. Tom
On May 19, 2025, at 7:56 AM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi!
I am dabbling with the alphafold interfaces command, and I cannot make sense of the data.
In my user case, the table synthesis produced by the command says:
Models Confident pairs #Res1 #Res2 4 23 12 12
opening the best model produces these relevant lines in the log
200 atoms, 188 bonds, 24 residues, 1 model selected
alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 maxPae 5.0 Found 14 residue or atom pairs within distance 4 with pae <= 5
in the csv, the same model has these relevant columns:
distance, max_pae, num_res1, num_res2, num_interface_res1, 4, 5, 246, 246, 20,
num_interface_res2, num_interface_res_pairs, num_confident_pairs, 20, 42, 23,
interface_res_num1, interface_res_num2 12 values 12 values
I am struggling a bit to reconcile all these numbers.
The 24 residues selected by chimera after opening are not anywhere else.
I suppose these are #Res1 + #Res2 of the synthesis (and interface_res_num1 + interface_res_num2 in the csv)?
Both the log synthesis and the csv report 23 as number of confident pairs, but the log message after opening best model says 14 residues (I assume these are those within the distance/pae constraint?)
Why Confident pairs is not #Res1 + #Res2?
I am also a little bit puzzled by the csv where I read num_interface_res_pairs = 42 and num_interface_res1, num_interface_res2 20 ( I was expecting either 21,21 for num_interface_res or 40 for num_interface_res_pairs.
I attach the prediction I was using for diagnosing the problem.
cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118 <o15305_a108e.zip>_______________________________________________ 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/