[Chimera-users] Map to CCP4 Style Mask

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 20 08:39:55 PDT 2017


Hi Martin,
You can set the threshold level with the “volume” command.  I’m not familiar with “ccp4 style mask file” (and as far as I know Chimera doesn’t write mask files), but you can do the masking by the isosurface directly in Chimera with the “mask” command.

Example:
volume #0 level 0.02
mask #0 #0 model #1

That example has the trivial case of masking the volume by its own isosurface, but you can mask a map by the isosurface of some other map (or various surfaces created in different ways).  The “volume” and “mask” commands have lots of options, see:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

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

> On Oct 20, 2017, at 7:30 AM, Martin Lawrence <lawrence at chemistry.montana.edu> wrote:
> 
> Hi All,
> Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file?
> Thanks,
> Martin




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