[Chimera-users] how to generate good STL code for atoms display

Tom Goddard goddard at sonic.net
Thu Apr 7 16:35:27 PDT 2016


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
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