On Tue, Oct 4, 2016 at 11:28 AM, Spencer Bliven <spencer.bli...@gmail.com>
wrote:
> I've done a bit of 3D printing of proteins. I found links in the previous
> thread VRML2 export and edu pymol
> <https://sourceforge.net/p/pymol/mailman/message/35012597/>helpful.
>
> STL is the best supported format for the printers, but since it's not
> supported by pymol I've used VRML2 (.wrl). Fortunately free tools to
> convert are readily available. A bigger problem is ensuring that the
> exported geometry is manifold. I've always had to do some cleanup in a 3D
> modeling program (e.g. blender, sketchup, etc) to get 3D printing software
> like Slic3r to accept it. Algorithms to automatically merge all geometry
> would be really nice if you're improving Jmol's export functionality.
>
Yes, the "hole" problem is important. The thing that happens with Jmol is
that when a cylinder penetrates a sphere, that causes a crossing that has
to be fixed. I was hoping someone has an easy fix for that, but now I see
that the printer-related software is used to this and can take care of it.
So perhaps it is not something that we need to worry about in PyMOL or
Jmol.
It seems to me PyMOL could easily implement STL. It is an extremely simple
format. I added this last week to Jmol in an afternoon. The problem I had
was that a lot of 3D printing software does not recognize the higher-level
objects such as Cylinder, Cone, and Sphere that are in VRML. So although
they may say they are "VRML 2.0" that's not really the case. They are "VRML
2.0 basic". But once that was done, it was a snap. Just a few extra lines
of code once the WRL is working. The files are big, though!
>
> You don't need to worry about support material. That should be handled by
> the slicing software, since it needs to know about the printer hardware to
> be generated efficiently.
>
>
It's not "support material" as much as "support". Jmol (and I think Pymol)
has automatic strut construction for proteins. This is critical for some
modeling materials that are brittle, such as colored silica like they use
at the Center for Biomolecular Modeling.
> -Spencer
>
>
> On Mon, Oct 3, 2016 at 9:50 PM, Sampson, Jared M. <
> jms2...@cumc.columbia.edu> wrote:
>
>> Hi Bob -
>>
>> I also haven't done much of anything with 3D printing myself, but having
>> worked on the COLLADA exporter as one of my POSF fellowship projects, I can
>> share some info about the formats themselves and what data is being
>> included in the output files.
>>
>> > Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary],
>> other)
>>
>> The list on the Save wiki page is fairly complete. It reads:
>>
>> "The file format is autodetected if the extension is .pdb, .pqr, .mol,
>> .sdf, .pkl, .pkla, .mmd, .out, .dat, .mmod, .pmo, .pov, .png, .pse, .psw,
>> .aln, .fasta, .obj, .mtl, .wrl, .idtf, .dae, or .mol2."
>>
>> The 3D formats among these (that I recognize, anyway) are .obj (Wavefront
>> Object), .mtl (Wavefront Material), .wrl (VRML2), .idtf (Intermediate Data
>> Text Format), and .dae (COLLADA).
>>
>>
>> > Q: Does the generation of these include algorithms for ensuring closure
>> or for stitching together objects in order to not have ragged overlap?
>>
>> I'm not sure what you mean by "stitching together objects," but in
>> general, as long as you have fully closed surfaces, it shouldn't be an
>> issue. The only situation I can think of that would be problematic is if
>> you had clipping panes that cut through the object's representation and end
>> up with a hollow, infinitesimally thin shell. That would be pretty
>> difficult to print. :)
>>
>> > Q: What is needed to add support struts so that the model is connected
>> and strong enough?
>>
>> No, this is related to what Paul was asking about recently. My guess is
>> some 3D printing software or sites might have more appropriate tools to put
>> these in, although you could do it manually (and probably quite tediously)
>> with CGO cylinders or distance dashes with dash_gap = 0 if you know the
>> orientation you want to use.
>>
>> > Q: If features are not amenable to printing (labels, perhaps?), are
>> they automatically ignored? Need to be manually removed?
>>
>> As far as I know, none of the supported 3D formats include labels in
>> their exported data. Each one has its own implementation, but in general,
>> representations stored within PyMOL as triangle meshes (surfaces and
>> cartoons, primarily, although you can get everything as triangles with `set
>> use_shaders, 0`) are supported by all of them. The COLLADA exporter also
>> handles spheres, cylinders, sausages (i.e. rounded cylinders, such as ) and
>> cones. VRML2 includes spheres, cylinders and sausages. The .obj exporter
>> has a bug in sphere export that I looked at about a year ago but got busy
>> and didn't actually follow through on. The others I don't know enough
>> about to comment, but hopefully this gets you on the right track.
>>
>> If you want to look further into it, check out the
>> RayRender{VRML2,IDTF,ObjMtl,COLLADA} functions in layer1/Ray.cpp or
>> layer1/COLLADA.cpp and look for cPrimTriangle, cPrimSphere, etc. for the
>> various primitive types.
>>
>> Hope that helps!
>>
>> Cheers,
>> Jared
>>
>>
>>
>> >
>> > Thanks,
>> >
>> > Bob Hanson
>> > ------------------------------------------------------------
>> ------------------
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>>
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>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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