[Chimera-users] [chimera-dev] suggestions for better STL export - remove internal, reduce atom vertices

Jakob Suckale jakob.suckale at uni-tuebingen.de
Mon May 9 00:32:31 PDT 2016

Dear all,

A follow up on Tom's suggestion. I have tested MeshLab. It does indeed have
functions that can be used to reduce internal surfaces (
https://www.youtube.com/watch?v=9EHJQd3SREE) but it's far from a good
solution. It is based on assigning a value to vertices based on visibility
(Ambient Occlusion) and then removing the ones that have low scores. In a
ribbon model, however, it often opens holes for example on the inside of a
helix and it leaves many internal structures untouched.

All the best,


On 15 April 2016 at 21:29, Tom Goddard <goddard at sonic.net> wrote:

> Hi Jakob,
>   We discussed the excessive STL vertices in atoms and bonds last week and
> I put a fix into the daily build and release candidate.
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html
> Apparently you are not using those versions since your images show the
> high vertex density.  I’ve attached an image using the current Chimera
> release candidate that shows reasonable vertex density.
>   Unfortunately eliminating internal structures and stitching together
> meshes for atoms, bonds and ribbons at the seams is very difficult.  Yes
> $10000 CAD software packages can do it but we don’t have the resources to
> solve that problem.  Since every 3d printer has to deal with this problem I
> expect the printer software to be able to handle it, but perhaps it is too
> hard a problem for the 3d printer companies as well.  Perhaps there is free
> software that can eliminate internal structures and stitch mesh
> intersecting edges together, I have not researched it — I’d start looking
> at MeshLab.
> Tom
> On Apr 15, 2016, at 4:33 AM, Jakob Suckale wrote:
> Dear Chimera developers,
> Chimera has the great feature of STL export, very useful for 3D printing
> models for research and teaching. May I make two suggestion to improve this
> feature even further.
> 1 - Remove invisible internal and therefore unnecessary structures.
> Chimera generates a lot of internal structures that complicate printing
> and are pointless for STLs. This includes inside surfaces at the end of
> ribbon cartoons (red below).
> <Screen Shot 2016-04-15 at 13.24.44.png>
> as well as copious amounts of invisible internal surfaces for wire and
> ball and stick models.
> <Screen Shot 2016-04-15 at 13.27.36.png>
> If these were automatically removed, STLs would not only be much smaller
> but also much easier to print without remashing.
> 2 - Reduce the number of vertices for atom models.
> Ribbon conversion to vertices is already good, but as can bee seen above
> atom models are converted using far too many vertices inflating the
> resulting STL files. I'm aware that this has been discussed and listed
> previously as a bug but the problem remains and makes for difficult to use
> STLs and bad 3D prints.
> Best regards,
> Jakob Suckale, PhD
> Lecturer in Biochemistry
> University of Tübingen
> +49-7071-29-73363
> _______________________________________________
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> Chimera-dev at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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