Hi Oliver, This is easy to do with the existing "volume onesmask" and "volume falloff" commands. For example open 1080 from emdb shape cylinder radius 50 height 100 volume onesmask #2 ongrid #1 volume falloff #3 I don't think it is worthwhile to cram all the onesmask and falloff options into the shape command. You might also use the "volume gaussian" command instead of the "volume falloff" command to soften the edges. The volume falloff command will not modifiy the ones region, only the zeros outside the boundary, while the volume gaussian command will modify inside and outside the mask. Tom
On Jan 17, 2024, at 8:22 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Would it be possible in a future release to add an option to the "shape" command to output the shape as a map (filled with 1s inside the shape, zeroes outside, maybe with an optional soft edge and an ongrid option)?
This would be very convenient for making simple geometrical masks for cryoEM (e.g soft cylindrical masks for classification within a nanodisc).
I currently do this using "shape cylinder", use the cylinder to mask the map, and then gaussian filter the resulting masked map to the point where I can choose a threshold that conforms to the shape, but having a way to do the same thing more directly would be very nice to have.
Cheers Oli _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/