[PyMOL] Leap Motion
Hey :) We've been playing recently with a Leap Motion controller for PyMol and are now wondering how we would emulate a mouse click event, based on the screen coordinates. Does anyone know? Thanks in advance, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] 3D printing
Can someone give me a summary of capabilities and limitations in PyMOL re 3D printing? For example: Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary], other) Q: Does the generation of these include algorithms for ensuring closure or for stitching together objects in order to not have ragged overlap? Q: What is needed to add support struts so that the model is connected and strong enough? Q: If features are not amenable to printing (labels, perhaps?), are they automatically ignored? Need to be manually removed? Thanks, Bob Hanson -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 3D printing
Bob, I've just started 3D printing myself. I've been focusing on complex ball-and-stick models (I posted some questions about WRL output not too long ago), as there seems to be very few people doing these type of models. By most accounts, doing surfaces or cartoons is more straightforward, and in many cases you can find things already on the NIH 3D print exchange, or send something through their pipeline. Questions answered as best as I know: On 10/03/2016 01:02 PM, Robert Hanson wrote: Can someone give me a summary of capabilities and limitations in PyMOL re 3D printing? For example: Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary], other) WRL is the best bet for export. It only exports what is in the scene. Q: Does the generation of these include algorithms for ensuring closure or for stitching together objects in order to not have ragged overlap? No. This has to be done manually and is the biggest pain for any output from the visualization software I have tried. You might be able to dump it into one of the available online tools, but I have never really tried. I've developed a Blender python script to work with PyMOL output VRML files specifically for ball-and-stick models. It is a work in progress but it does model clean up, manifolding, and if desired it can manually put pins/holes in certain cylinders/spheres so models can be printed as separate pieces and stuck together after the fact. I'd be happy to share it with anyone interested. Q: What is needed to add support struts so that the model is connected and strong enough? Really has to be done manually. NIH pipeline may have ways of automating this. For VRML output, one can just use distance measurements with dash_gap set to 0 to make struts. I use this for H-bonding as well. Q: If features are not amenable to printing (labels, perhaps?), are they automatically ignored? Need to be manually removed? Just hide them before exporting to VRML format Thanks, Bob Hanson -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 3D printing
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
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org!
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