Dear Jiaqiao Zhou, You can label the selected pseudobonds by the two residues (name and number) but the command is very long and ugly. I did not figure this out by myself... The following command should be all one line even though e-mail display may break it into more than one line, and plain text with plain quotation marks: label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" You would have to select the pseudobonds before that, e.g. if those are the only pseudobonds you have: sel pbonds The parts between the {} should stay the same but you could change the formatting like spaces and the word "to" that are outside of them. The four things inside {} are the name and number of the first residue and the name and number of the second residue. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html> The distance in "alphafold contacts" is "any interresidue distance," i.e., all atom-atom distances between the two residues are used and the shortest one determines whether it is within your specified distance or not. However, the pseudobond is drawn between alpha-carbons, so its length is not exactly the same as the shortest distance between the residues. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 12, 2022, at 7:50 AM, Jiaqiao Zhou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimerax users,

I am trying to analyze the results of AF2 predictions. I used the "alphafold contacts" command to the interfacing residues, then several pseudobonds are displayed.

"label sel pseudobonds" shows the length of the bonds, but I want to show the residue name the number that makes the pseudobonds.

Actually, I found that in the label mode of right mouse, it shows the residue name and the number. However, I have to do it one by one. So I am wondering if there are any easier ways.

Another question is about the "alphafold contacts" command itself, I want to know the definition of "distance of residues". Is it the distance of the centroid, the average distance of heavy atoms of the residues. or some other ways of determining the distance between two residues?

Thanks in advance.