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/command... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > 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/command... > 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