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

Jakob Suckale jakob.suckale at uni-tuebingen.de
Fri Apr 8 02:19:40 PDT 2016

Hi David,

Yep, you recalled that well despite the convoluted name. It does help
with overall simplification but it does that for all structures
proportionally and ribbons are well converted. It's just the atom
models that are excessive.

What I cannot do yet in Meshlab is get rid of all these pointless
internal structures. The 5-membered ring in the attachment for example
is full of invisible vertices inside that inflate the file size. There
are ways to partially remove internal structures with Meshlab
(http://bit.ly/1Tyzz1u) but they don't do a very good job because they
typically remove some of the outer ribbon surfaces as well creating
hole that need to be filled.

All the best,


On 7 April 2016 at 23:01, David Bhella <David.Bhella at glasgow.ac.uk> wrote:
> I use meshlab for this I am not in front of my mac just now but from memory the filter is quadratic edge collapse decimation (or something like that). It works well to reduce the poly count.
> E-mail me if you want help trying it.
> Another useful tool is netfabb to repair stl files by removing unwanted shells and fixing non-manifold maps. Lately I have found surfaces from chimera don't suffer from this as much as they used to....
> Sent from my iPad
>> On 7 Apr 2016, at 21:17, Greg Couch <gregc at cgl.ucsf.edu> 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 <jakob.suckale at 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
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