Export options for x3d2stl
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.
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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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> 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. From: Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> Date: Monday, December 16, 2013 3:06 PM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>>, "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hurt, Darrell (NIH/NIAID) [E]