[Chimera-users] Hollow Sticks When Exporting as STLs?

Tom Goddard goddard at sonic.net
Tue Aug 17 11:49:47 PDT 2021

Hi Josh,

  You are right that Chimera makes bonds as cylinders with no end caps and 3D printer software sometimes has trouble with that.  If the cylinders had end caps then they would probably be treated as solid for 3D printing but this slows down rendering by adding end caps that cannot be seen, so Chimera does not do that.  Even with end caps, the atom sphere intersects the bond cylinder and in the past I have seen 3D printers make the overlap between the two hollow (using old uPrint printer).  What the 3D printer software really wants is a single closed mesh.  That is computationally very difficult to produce in molecular visualization software so I don't know any that do it.  Instead post processing software needs to fix the mesh problems.  I don't know what the current best methods are to do that -- it was very difficult to achieve several years ago when I used to make 3D prints.

  Here is a nice web page on Chimera 3D printing

	https://openwetware.org/wiki/UCSF_Chimera_for_3D_Printing <https://openwetware.org/wiki/UCSF_Chimera_for_3D_Printing>

  The NIH Print Exchange are experts at making printable models using Chimera -- you might use their pipeline or read about or ask how they do it.

  I see some old 2013 info when I google for chimera 3d print ball and stick.

  I think ultimately this is a hard problem to solve and you have to find the right software that can make good closed meshes, or good toolpath software that can deal with meshes that have holes.


> On Aug 17, 2021, at 10:10 AM, Josh Moon via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I hope to make this question as direct and simple as I can!
> When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my “stick” portions are hollow.  This creates thin, weak walls for 3D printing.  I’ve included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure.
> What am I doing incorrectly?  Is there something I can do in Chimera to export a solid object with no “hollow tubes.”  Fixing this with 3d programs can be time consuming.
> Sincere thanks,
> Josh
> -----------------------------------------
> Josh Moon, Ph.D. (he/him/his)
> Educational Technology Specialist
> Kalamazoo College
> (269) 337-7415
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