[Chimera-users] Export options for x3d2stl

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Dec 16 12:15:43 PST 2013


Hi Greg,

Thanks for your quick reply. You're certainly right about the problems with overlapping triangles and 3D printers.

No problem. I just wanted to see if there might be some (as yet) undocumented way to control the export. I'll do it outside of Chimera through a wrapper script. (Sorry about the Blender slip-up — I've got a bunch of things whirling through my head right now…).

Cheers,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>

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From: Greg Couch <gregc at cgl.ucsf.edu<mailto:gregc at cgl.ucsf.edu>>
Date: Monday, December 16, 2013 3:06 PM
To: Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>, "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Export options for x3d2stl

I assume you meant just run outside of Chimera.  x3d2stl would
presumably always be run outside of Blender.

And to answer your question, right now there is no way within chimera to
give options to x3d2stl, nor any of the other converters -- X3D output
is the only completely native format.  So you need to first export the
X3D output, then run x3d2stl separately with the options you require.

As you may have deduced, the -r option sets the tessellation resolution,
roughly the number of vertices per unit area, and -c says to cap all
primitives.  Since the sphere and cylinders intersect that chimera
generates to represent atoms and bonds, the STL triangles also
intersect.  And intersecting triangles cause problems for some 3D
printer software, so you might need to limit the output to just
surfaces.  Some 3D printer software takes VRML input, so for those
printers, I'd recommend using Chimera VRML output, and let the 3D
printer software do the conversion to STL.

     HTH,

     Greg

On 12/16/2013 10:55 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Chimera friends,

Here's the second question of the day. Thanks for your patience with me.

When I export the scene as an STL (for 3D printing), I think what happens is that Chimera outputs first an X3D file and then runs the utility program "x3d2stl" to create the STL. The X3D file is about 5 MB, but the STL is about 100 MB. I understand that much of this size inflation is because the "primitives" in X3D have to be converted to mesh objects for STL. However, when I look at the STL file, the meshes derived from the primitives are finer than I really need.

I find that I can "get away with" a coarser meshification by using x3d2stl on the command line:

x3d2stl -c -r 2 -o sticks.stl < sticks.x3d

If I want to export the scene via the command line within Blender, is there any way to issue options to x3d2stl? Or should I just run x3d2stl outside of Blender?

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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