Hi Amita,
First be aware that  "alphafold contacts" is not primarily meant to identify contacts but instead to show with colored lines the alphafold confidence values (PAE) in the relative positions of pairs of residues.   The colors of the lines show the PAE values.  The "distance 3" part merely limits where the lines are drawn to residue pairs that are close together.

If you still want that information, given the description above, you can use the "outputFile" option of "alphafold contacts" to write a list of the residue pairs and their closest distance, as described in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts>

This outputFile option was also described in a previous post:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/OILDSN4EDZTHTANX5RHTVNXFC3KYX3EE/>

However, in general:
If you just want to identify the atomic contacts in any structure regardless of whether it is from alphafold or not, it may be better to use the menu: Select... Contacts...  , see:
<https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
 
This approach uses either the "contacts" command or "interfaces" command depending on the options you choose, and you could also use either of those commands directly instead of via the menu.  The "contacts" command has a "saveFile" option to write a list of the contacting atom pairs and their distances.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

I hope this helps,
Elaine 
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

Begin forwarded message:

From: Amita Mohan via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Re: ChimeraX question
Date: April 16, 2024 at 9:18:18 AM PDT
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Reply-To: Amita Mohan <amimohan@sas.upenn.edu>

Hello Elaine,

I have a question, in chain A and chain B, I have identified the contact resides using the command ‘alphafold contacts /A to /B distance 3’. I want to write the chain A and B (for example /A Asn 431 — /B The 321) contact residues as file. How can also get the information on the blue and yellow interactions as well. I used the information you have provided in previous email, I can write only either chain but not the contact residue information that will help in protein-protein interactions. The example is provided in the below screen shot.

Thank you.

Amita

On Apr 2, 2024, at 4:30 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

info residues sel saveFile ~/Desktop/residue-list
Screenshot 2024-04-16 at 12.15.45 PM.png