From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Fri Jul 26 2019 - 15:19:02 CDT

Thank you Giacomo! This is exactly what I need!

On Fri, Jul 26, 2019 at 5:09 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>
> Giacomo
>
> On Thu, Jul 25, 2019 at 6:18 PM Bassam Haddad <bhaddad_at_pdx.edu> 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
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>