create mask from "shapes"
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
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@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
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
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
participants (2)
-
Elaine Meng
-
Roberto Marabini