[Chimera-users] Automatic struts for 3D printing?

Tom Goddard goddard at sonic.net
Fri Aug 16 15:14:54 PDT 2013


Hi Darrell,

  Here are some of the molecule models we have printed in plastic.

	http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html

and a description of the printer we used

	http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html

  Chimera does not currently have any tool to automatically add struts, although I've done this by hand in Chimera.  For instance the heptatis B virus pentamer on the above web page had part of an icosahedral cage made from cylinders underneath it to hold the proteins on the virus surface together.

  One thing you'll see is that all our printed molecules came from surface depictions in Chimera (made with molmap command).  I'm not sure if we successfully printed and ball and stick models via STL or VRML.  We tried years ago and I recall them falling apart because where the spheres and cylinders intersected it put no plastic.  Basically an atom sphere and bond cylinder are two surfaces and for points inside two surfaces (or any even number of surfaces I think) the printer places no plastic.  So overlapped cylinders and spheres didn't hold together.  This seems to be a printer driver issue -- how it takes a surface and makes a solid out of it.  I don't know that we've tried with our newer printers at UCSF -- maybe it works now.

  Have you successfully printed ball and stick models exported from Chimera?  What kind of printer?

  Now about automatically adding struts -- probably would not be hard.  The struts code I saw online

	http://idp1.force.cs.is.nagoya-u.ac.jp/jmol/src/org/jmol/modelsetbio/AlphaPolymer.java

didn't have a clear description of the algorithm the use, but it would just take an hour to study it.  I could see aiming to add struts that 1) are cylinders between atoms, 2) are short, 3) make the whole model one connected piece, 4) make every contiguous N (50) residues connected in at least 3 places (2 probably being continuations before and after and one being a crossbridge) to other residues for rigidity, 5) not put connections at the ends where they would be easily confused for real biological connections, 6) struts should not look like real bonds -- maybe make them fatter or better square cross-section.  Actually that rigidity constraint is more complex -- probably don't want to have two large pieces connected to each other through only one bond.

  I recall printing some ribbon models in ABS plastic with ribbon cross-section pretty small -- half a centimeter.  With 100 residues and no cross bridges the model is very flexible and easy to break.

  Could you provide a picture of a ball and stick model with struts to give a better idea of what you are shooting for?

	Tom


On Aug 16, 2013, at 2:32 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:

> Hi everyone,
> 
> We are assembling an open data portal or "exchange" for producing "ready-to-3D-print" files for biological molecules, EM data, and other imaging data using some automated pipelines. A little bit more on our project can be found here:
> http://www.hhs.gov/open/initiatives/ignite/3d-printing-exchange.html
> 
> A few years ago this came up on the "dev" discussion board:
> http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000800.html
> 
> In the email thread above, it mentions a script by George Phillips called "struts.py" that was modified for use in RasMol. I am familiar with his version of this script for PyMOL. It works very well and I have been using it for years. However, the VRML from PyMOL is sometimes buggy. I like the exports from Chimera much better, including the X3D2VRML and X3D2STL utilities. If I could get the same functionality of this "struts" script in Chimera, that would be one less thing I need to go to PyMOL for (the list is getting shorter and shorter!).
> 
> We're looking at doing it here, but I would welcome any contribution from the Chimera community if something already exists. Do you have anything? Is this script something of interest? Anyone interested in contributing to our "exchange" database/web portal? I would love any feedback you might have.
> 
> Thanks,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
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