[chimerax-users] inquiry about label the residues of pseudo bonds

[Elaine Meng]

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 at 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.