dear all, I have an object imported from segmentation in dragonfly that is quite jagged and rough looking. Is there a way to smooth the surface? When I try "surface smooth" that doesn't work because I guess it's looking for atoms/surface render. Is there a way to smooth .stl or .obj files? Thanks Jesse
Hi Jesse, In my tests today the "surface smooth" command works fine on an STL file. e.g. test.stl attached, example commands: open test.stl surface smooth #1 factor .5 iterations 5 hide #1 models See help for explanation of the parameters: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#smooth> The surface smooth command makes a new model #2 (unless you add "inplace true" to overwrite the original #1), so the old one is still shown unless you hide it, as in the example commands above. I do not have an obj file handy to test, but this command should work on any surface model. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2023, at 7:18 AM, Jesse Hansen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
dear all,
I have an object imported from segmentation in dragonfly that is quite jagged and rough looking. Is there a way to smooth the surface? When I try "surface smooth" that doesn't work because I guess it's looking for atoms/surface render. Is there a way to smooth .stl or .obj files? Thanks
Jesse
Dear Jesse, Another way to go about it, kinda inefficient but which can give nice results: Convert the object to a density volume using the command "volume onesmask": https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask then low-pass filter this volume using a Gaussian using "volume gaussian": https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#gaussian then you can threshold the resulting volume to a binary mask again (see "volume threshold") or save it back as an .obj or .stl file: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#threshold https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html Best wishes, -- Ricardo Diogo Righetto Em sex., 2 de jun. de 2023 às 18:05, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> escreveu:
Hi Jesse, In my tests today the "surface smooth" command works fine on an STL file. e.g. test.stl attached, example commands:
open test.stl surface smooth #1 factor .5 iterations 5 hide #1 models
See help for explanation of the parameters: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#smooth>
The surface smooth command makes a new model #2 (unless you add "inplace true" to overwrite the original #1), so the old one is still shown unless you hide it, as in the example commands above.
I do not have an obj file handy to test, but this command should work on any surface model.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2023, at 7:18 AM, Jesse Hansen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
dear all,
I have an object imported from segmentation in dragonfly that is quite jagged and rough looking. Is there a way to smooth the surface? When I try "surface smooth" that doesn't work because I guess it's looking for atoms/surface render. Is there a way to smooth .stl or .obj files? Thanks
Jesse
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participants (3)
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Elaine Meng -
Jesse Hansen -
Ricardo Righetto