From: Giacomo Fiorin (
Date: Fri Jul 26 2019 - 07:08:42 CDT

Hi Bassam, I haven't used it myself but I think that the "volX" and
"interpvolX" properties of atom selections can be used for this purpose:
$sel get interpvol0 ; # Returns the 1st volumetric map's values at each
atom position


On Thu, Jul 25, 2019 at 6:18 PM Bassam Haddad <> wrote:

> Hello All,
> I am trying to analyze some MD trajectories by comparing the individual
> side-chain locations to experimentally determined CryoEM densities. I want
> to write a script that essentially checks if a residue is at least 50% (50%
> of the residues atoms) within the .mrc (volume file) at a pre-determined
> iso-value.
> I can imagine doing something like this in Python using MDAnalysis &
> gridData, however I would much rather use TCL/VMD. Is this possible in VMD?
> Thank you in advance!
> Bassam Haddad

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD