Hi, thank you for the reply.

I noticed your reply in my spam mail 🥲. I wonder why there's no reply from the chimerax teams.
I have tried the command that you suggested and it worked like a charm. Thank you so much!

I have sent the same email again because I thought there was something wrong with the email due to no reply. 
I had already deleted it but in case you guys had received it, I apologize.

Thank you. Regards,
Aida.

On Thu, 26 Sept 2024 at 00:20, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Aida,
I don't think you want to use "info distmat" because it will give you all N X N distances for the N atoms (not just between drug atoms and protein atoms), and there is no cutoff option. It would always give you ALL of the distances.   Your second command is the one with correct syntax, but it will make such a huge output you can't easily look at it in the Log and so it would be better to also use the saveFile option.  However, it is not the right command to use for what you want to do.

Instead you should use the "contacts" command, because then you can define the two separate sets of atoms and only get the distances between them, and you can give a cutoff value.  There was a very similar example in a recent post to chimerax-users:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/LP5IZ7V7DMSEOFFZBXHTSFEYEAVOY4NR/>

In your case it would be something like this to list distances in the Log

contacts (protein & sideonly) restrict :dex distanceOnly 4.0 log true make false

If you wanted to save the results to a file, you would also include something like  "saveFile distances.txt"
If you wanted to draw lines on the 3D structure and label them with distance, you would use options "make true" and "showDist true"

The command and its options are described in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

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


> On Sep 25, 2024, at 8:50 AM, NUR AIDA SAKINAH via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi ChimeraX teams,
> Can you guide me to use the  atoms-spec for info distmat command.
> I want the output in chimerax log to list out distances between drug compound and the amino acids side chains and only display the distances below than 4 A.
>
> For now, what i have got, the output include distances between atoms in the drug itself and atoms in the amino acids itself. The command that i have try are:
>     •
> info distmat (protein & sideonly) | :dex ::num_distance< 4
>     • info distmat (protein & sideonly) | :dex
>     • info distmat (protein & sideonly) & (:dex) distance < 4
>
> Hope you could help me with this.
>
> Regards with thanks,
> Aida.