[Chimera-users] Mask Question in windows Chimera

[Elaine Meng]

Hi Jing,
There is no Mask button in Volume Viewer -- as you found, you need to use the "mask" command.  Masking requires a volume (map) model and and surface model.  Sometimes the surface is the same model number as the map, if the surface you want to use for masking is the isosurface of that map.  Sometimes the surface is a different model number, e.g. if you were masking by the molecular surface of an atomic model, or the isosurface of a different map.  It is not possible to give you an exact command since I don't know exactly what you are trying to do, or the model numbers of what you have.

If your map is #1 and surface is also #1

mask #1 #1

...but there are lots of other options you might want also want to include in that command.  See the "mask" help. 
<https://www.rbvi.ucsf.edu/home/meng/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 Jul 4, 2022, at 5:45 AM, Zhang, Ruojing via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> To whom it may concern,
>       Hello, this may sound like a silly question. May I ask how to use Mask in Volume? For some unknown reasons, I could not find the Mask button in Volume Viewer and neither in the tool taskbar. The input files are pdb and mrc file. I used Fit in Map to align structure and map. Then I selected the whole structure. When I went back to mask the map, I could not find the Mask button in Volume Viewer. When I tried to run in the command line (mask), it shows "missing required arguments: Volume, SurfaceSpec". Could you please help?
>       Thank you
> Jing