Thanks for the information Elaine. This will be very useful. Roberto On Fri, Jul 23, 2021 at 5:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

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

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On Jul 23, 2021, at 1:25 AM, Roberto Marabini via ChimeraX-users < chimerax-users@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