Hi, I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach? Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this. Best, Saren -- Saren Tasciyan /PhD Student / Sixt Group/ Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria
Hi Saren, As far as I know the STL has the same mesh resolution (same triangulation) as the surface had in ChimeraX, although the surface in ChimeraX may look smoother because of the surface normals and how the lighting is done. How to use smaller triangles in the surface in ChimeraX depends on the type of surface: (A) If it is a molecular surface you can control it with the "gridSpacing" option of the "surface" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> (B) If it is a volume surface (e.g. density map isosurface) there are several options of the "volume" command having to do with surface subdivision and smoothing, and whether square mesh is shown, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> You would also want to use "step 1" for the full resolution of the map data: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> 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 15, 2021, at 3:48 AM, Saren Tasciyan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach?
Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this.
Best,
Saren
<ffmmfhbpapbfadmd.png>
<bfamkfhfkccijeli.png>
--
Saren Tasciyan PhD Student / Sixt Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria
Hi Elaine, Thanks a lot. surface ... gridSpacing did the trick In this case it was about a molecular surface. Best, Saren On 15.06.21 17:22, Elaine Meng wrote:
Hi Saren, As far as I know the STL has the same mesh resolution (same triangulation) as the surface had in ChimeraX, although the surface in ChimeraX may look smoother because of the surface normals and how the lighting is done.
How to use smaller triangles in the surface in ChimeraX depends on the type of surface:
(A) If it is a molecular surface you can control it with the "gridSpacing" option of the "surface" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
(B) If it is a volume surface (e.g. density map isosurface) there are several options of the "volume" command having to do with surface subdivision and smoothing, and whether square mesh is shown, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> You would also want to use "step 1" for the full resolution of the map data: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
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 15, 2021, at 3:48 AM, Saren Tasciyan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach?
Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this.
Best,
Saren
<ffmmfhbpapbfadmd.png>
<bfamkfhfkccijeli.png>
--
Saren Tasciyan PhD Student / Sixt Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria -- Saren Tasciyan /PhD Student / Sixt Group/ Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria
Hi Saren, Elaine is right that the STL mesh has exactly the same set of triangles that is being shown in ChimeraX. The faceted appearance of the STL is because that file format does not contain surface normal vectors that allow graphics rendering to smooth the appearance. The most common use of STL format is for 3D printing and the the 3D printers don't have enough resolution to see those facets you see in the graphics, so for 3D printing you usually don't need to increase the subdivision of the surface. Tom
On Jun 15, 2021, at 9:04 AM, Saren Tasciyan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks a lot. surface ... gridSpacing did the trick
In this case it was about a molecular surface.
Best,
Saren
On 15.06.21 17:22, Elaine Meng wrote:
Hi Saren, As far as I know the STL has the same mesh resolution (same triangulation) as the surface had in ChimeraX, although the surface in ChimeraX may look smoother because of the surface normals and how the lighting is done.
How to use smaller triangles in the surface in ChimeraX depends on the type of surface:
(A) If it is a molecular surface you can control it with the "gridSpacing" option of the "surface" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
(B) If it is a volume surface (e.g. density map isosurface) there are several options of the "volume" command having to do with surface subdivision and smoothing, and whether square mesh is shown, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf> You would also want to use "step 1" for the full resolution of the map data: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling>
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 15, 2021, at 3:48 AM, Saren Tasciyan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach?
Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this.
Best,
Saren
<ffmmfhbpapbfadmd.png>
<bfamkfhfkccijeli.png>
--
Saren Tasciyan PhD Student / Sixt Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria -- Saren Tasciyan PhD Student / Sixt Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria
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participants (3)
-
Elaine Meng -
Saren Tasciyan -
Tom Goddard