how to generate good STL code for atoms display
Dear chimeras, Does anybody know of a good way to generate lean STL code for atom/bond display? Take this example. I'm generating STLs to 3D print GFP. Exporting the ribbon of the beta barrel generates an ok STL of 6.8MB. However, exporting the wire atom display of the chromophore generates a horribly inflated STL of 13.7MB - almost twice the ribbons file despite the tiny size (see screenshot attached). Printing the chromophore is problematic since it contains a lot of weird internal structures instead of being a clean surface model of the wireframe. A netfabb repair of the chromophore STL Looking forward to your expert ideas. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363
Sorry, the message was truncated. This is the missing part. A netfabb repair of the chromophore STL does significantly simplify the model and reduce the file size from 13.7 to 5.7 MB indicating that there's a lot of room for improvement in the STL export esp. of atom models. On 4 April 2016 at 11:54, Jakob Suckale <jakob.suckale@uni-tuebingen.de> wrote:
Dear chimeras,
Does anybody know of a good way to generate lean STL code for atom/bond display?
Take this example. I'm generating STLs to 3D print GFP. Exporting the ribbon of the beta barrel generates an ok STL of 6.8MB. However, exporting the wire atom display of the chromophore generates a horribly inflated STL of 13.7MB - almost twice the ribbons file despite the tiny size (see screenshot attached). Printing the chromophore is problematic since it contains a lot of weird internal structures instead of being a clean surface model of the wireframe. A netfabb repair of the chromophore STL
Looking forward to your expert ideas.
All the best,
Jakob
Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363
Hi Jakob, One way to reduce the number of STL triangles generated is to lower the subdivision amount in the graphics quality section of the Effects dialog in Chimera. Another way is to load the STL output into the open-source MeshLab program, http://meshlab.sourceforge.net/, and use its tools to simplify the mesh. I have not that, so if someone has done that, please chime in, and describe which MeshLab filters to use. You may need to use both techniques to make 3D printer software work. If your 3D printer takes VRML input, I would recommend using Chimera's VRML output instead. HTH, Greg On 04/04/2016 05:13 AM, Jakob Suckale wrote:
Sorry, the message was truncated. This is the missing part.
A netfabb repair of the chromophore STL does significantly simplify the model and reduce the file size from 13.7 to 5.7 MB indicating that there's a lot of room for improvement in the STL export esp. of atom models.
On 4 April 2016 at 11:54, Jakob Suckale <jakob.suckale@uni-tuebingen.de> wrote:
Dear chimeras,
Does anybody know of a good way to generate lean STL code for atom/bond display?
Take this example. I'm generating STLs to 3D print GFP. Exporting the ribbon of the beta barrel generates an ok STL of 6.8MB. However, exporting the wire atom display of the chromophore generates a horribly inflated STL of 13.7MB - almost twice the ribbons file despite the tiny size (see screenshot attached). Printing the chromophore is problematic since it contains a lot of weird internal structures instead of being a clean surface model of the wireframe. A netfabb repair of the chromophore STL
Looking forward to your expert ideas.
All the best,
Jakob
Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jakob, This is a bug in the Chimera 1 stl export reported a few years ago but never fixed. http://plato.cgl.ucsf.edu/trac/chimera/ticket/13183 It was outputing 20,000 triangles for each sphere, a bit excessive. I’ve fixed the code so it produces about 100 times fewer triangles. The “subdivision quality” setting mentioned in the previous email actually does not effect the STL output. So there is no way to control the number of triangles by setting a parameter. This same problem was discussed a few years ago and a way to control the number of triangles was explained in that mailing list discussion http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010045.html But you can just get tomorrow’s daily build (or the 1.11 release candidate) and it should produce a much smaller file. Tom
On Apr 7, 2016, at 1:09 PM, Greg Couch wrote:
Hi Jakob,
One way to reduce the number of STL triangles generated is to lower the subdivision amount in the graphics quality section of the Effects dialog in Chimera.
Another way is to load the STL output into the open-source MeshLab program, http://meshlab.sourceforge.net/, and use its tools to simplify the mesh. I have not that, so if someone has done that, please chime in, and describe which MeshLab filters to use.
You may need to use both techniques to make 3D printer software work. If your 3D printer takes VRML input, I would recommend using Chimera's VRML output instead.
HTH,
Greg
On 04/04/2016 05:13 AM, Jakob Suckale wrote:
Sorry, the message was truncated. This is the missing part.
A netfabb repair of the chromophore STL does significantly simplify the model and reduce the file size from 13.7 to 5.7 MB indicating that there's a lot of room for improvement in the STL export esp. of atom models.
On 4 April 2016 at 11:54, Jakob Suckale wrote:
Dear chimeras,
Does anybody know of a good way to generate lean STL code for atom/bond display?
Take this example. I'm generating STLs to 3D print GFP. Exporting the ribbon of the beta barrel generates an ok STL of 6.8MB. However, exporting the wire atom display of the chromophore generates a horribly inflated STL of 13.7MB - almost twice the ribbons file despite the tiny size (see screenshot attached). Printing the chromophore is problematic since it contains a lot of weird internal structures instead of being a clean surface model of the wireframe. A netfabb repair of the chromophore STL
Looking forward to your expert ideas.
All the best,
Jakob
Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (3)
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Greg Couch -
Jakob Suckale -
Tom Goddard