[Chimera-users] Measure unmodeled density

[Elaine Meng]

Hi Chen,
Not a single command, but may be possible with a few steps.

(A) somehow remove the density for the modeled part to create a map that just has the unmodeled density
(B) set contour level of the unmodeled-density map as you like, then use command “measure volume” to measure isosurface-enclosed volume
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#volume>

I’m guessing by “modeled” you mean that you have atomic structures fitted in.  In that case, two ways that might work for part “A” are:

- color all the atomic structures (could be all the same color), select all the atomic structures, use Color Zone and its “Split Map” button. The “unzone” part will be one of the resulting maps.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

- simulate density of atomic structures with “molmap” and use “vop subtract” to subtract it from the density, creating a new map of the unmodeled part.  Might be tricky to decide what resolution value to use with molmap.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

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

> On Feb 12, 2019, at 4:30 PM, Chen Sun <sun647 at purdue.edu> wrote:
> 
> Dear Chimera users,
> 
> I have a map with extra density in it and I'd like to know the volume of the extra density. So is there an existing command in Chimera that can measure the volume of unmodeled density?
> 
> Best regards,
> Chen
> Chen Sun
> Department of Biological Sciences
> Purdue University
> Hockmeyer Hall of Structural Biology
> 240 S.Martin Jischke Dr.
> West Lafayette, IN 47907
> 
> "The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts. --Bertrand Russell"