[chimerax-users] create mask from "shapes"

[Elaine Meng]

Hi Roberto,
Yes, you can mask with a shape.  The "shape" command creates a surface model, and then you can use any surface model in the "volume mask" command.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask>

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 23, 2021, at 1:25 AM, Roberto Marabini via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
>     It is possible to create a mask from a shape?. For example from the result of  "shape icosahedron".
> 
>     If the command does not exist I guess I may create it as follows
> 
> * the input would be the 3D map to be masked and the shape to be used as mask
> * request all the (varray, tarray) from the shape.
> * from varray,tarray build the  triangles that define the surface of the shape
> * for each triangle create the normal vector
> * multiply each normal vector by the position of each voxel (dot product)
> * keep those voxels that have negative dot products for all the triangles.
> 
>   thanks for the help