Dear Elaine and dear Moritz,

 

Thank you very much for your suggestions! Especially the hack to just use molmap and a single atom is such a fun exploit.

I eventually found a solution and it is also easy. As you can use this to generate masks in various fun shapes, I will share it here.

  1. Create a sphere using ‘shape sphere X’ X being the radius (In order to generate your favorite geometric shape of choice, please see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html).
  2. Move the surface model via ‘move model’ functionality.
  3. Create a map with values of 1 bounded by your surface via ‘volume onesmask #Y onGrid #Z”. Y being the volume to be masked and Z your surface model (see https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask).

Now you have a binarized volume to be used as a mask after adding a soft mask.

 

Best,

Lorenz

 

………………………………..

Lorenz Grundmann

PhD Student

M +43677/64603163

Icon Description automatically generated

 

lorenz.grundmann@imp.ac.at

www.imp.ac.at 

 

IMP

Research Institute of Molecular Pathology

Campus-Vienna-BioCenter 1

1030 Vienna, Austria

 

Part of Vienna BioCenter

 

 

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Wednesday, 9. August 2023 at 19:56
To: Grundmann,Lorenz Emanuel <lorenz.grundmann@imp.ac.at>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Spherical mask

Yet another related approach is that the Map Eraser tool erases within a sphere that you can easily size/position interactively:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html>

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

>
> > On Aug 9, 2023, at 2:13 AM, Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> >
> > Dear chimerax-team,
> > 
> > I am looking into a possibility to generate a spherical volume in chimerax that I can then use as a spherical mask for focused 3D classifications and signal subtractions. For my specific need, a sphere would be the ideal shape.
> > So far I managed to generate a surface model using the ‘shape sphere’ command, to place it to the region of interest and resampling it onto the coordinate system of my protein of interest.
> > Is there any possibility to transform the surface model into a (binarized) volume?
> > 
> > Best,
> > Lorenz