Hi Elaine,

This helped wonderfully!

I was curious if there is any convenient way to store the log output/save the output of "volume measure" as part of a python script? I have to run these calculations on a few hundred files so wanted to look for a way to automate it if possible?

Thank you for any help you can provide and thanks again for all the help you have already provided!

Best,
John
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Monday, January 27, 2025 6:16 PM
To: John Watters <jwatters@rockefeller.edu>
Cc: hu.qi--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Question about Surface Volume Overlap Calculation
 
Caution: External email

Hello John,
An approximate approach would be to get molecular surfaces on them separately, measure volume enclosed in each, then make a molecular surface that encloses both and measure its volume, and subtract the former from the latter.
 
See commands: surface (including "enclose" option), measure volume
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html__;!!M59pwtRysTUf!Z3prJ15zNXqEcv9Nsu_9iy43Ex2Z5CjqdV4Tlh7eYr_v1UXgaGpD0rmbCSJqL88cTDPQ1K717MU7uqaW-RHK8CU$ >
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html*options__;Iw!!M59pwtRysTUf!Z3prJ15zNXqEcv9Nsu_9iy43Ex2Z5CjqdV4Tlh7eYr_v1UXgaGpD0rmbCSJqL88cTDPQ1K717MU7uqaWdOClB_s$ >
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html*volume__;Iw!!M59pwtRysTUf!Z3prJ15zNXqEcv9Nsu_9iy43Ex2Z5CjqdV4Tlh7eYr_v1UXgaGpD0rmbCSJqL88cTDPQ1K717MU7uqaWqBOo-2I$ >

Example:

open 4hhb
surf
measure volume #1.2
measure volume #1.3
surface enclose /A,B & protein
measure volume #1.2

... that calculates molecular surfaces separately for 4hhb chains A-D, measures volumes for A and B (reported in Log), creates a new surface that is for the protein chains in A and B combined, measures again (again reported in Log).

It is only approximate because molecular surface is a smoothed solvent-excluded surface (SES), so you're not exactly getting a VDW overlap volume.  What you'd really want is VDW volumes, not SES-enclosed volumes.  But I can't think of a way to get the VDW volume of a set of atoms in ChimeraX.  Theoretically SES with zero radius probe would get it, but this calculation does not work for various reasons.  The smallest probe radius I could use and still get a surface instead of bits was about 0.3 Angstrom.

The ChimeraX "contacts" or "clashes" command reports the exact amount of VDW overlap btween pairs of atoms, but that is a linear (distance) measure.  So another possible measure would be the sum of all pairwise VDW overlaps between the two sets of atoms, but I realize it is not as intuitive as a volume value.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html__;!!M59pwtRysTUf!Z3prJ15zNXqEcv9Nsu_9iy43Ex2Z5CjqdV4Tlh7eYr_v1UXgaGpD0rmbCSJqL88cTDPQ1K717MU7uqaW6Qzl_RI$ >

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 Jan 27, 2025, at 2:46 PM, John Watters via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> I was wondering if anyone had any tips/tricks/useful functions for quantifying the volume of the overlap between two surfaces in ChimeraX? I am looking specifically to make a metric to compare steric clashes of molecules in different orientations.
>
> Thank you for any help you can provide!
>
> Best,
> John