[Chimera-users] Chimera - ball and stick - 3D printing

Tom Goddard goddard at sonic.net
Tue Jun 18 10:42:44 PDT 2013


Hi Francois,

 Here are some thoughts about printing your ball and stick 2beg model.  You could try displaying in ball and stick style, show hydrogen bonds (command "hb"), make the hydrogen bonds sticks instead of lines (menu Tools / General Controls / PseodoBond Panel, click hydrogen bonds line, press Select the Actions / Atoms / Stick), then export as STL (File / Export).  Your printer may have a problem with this file because it produces lots of sphere and cylinder surfaces instead of a single closed surface.  Our uPrint printer seems to fill no plastic between two surfaces that intersect (e.g. a sphere and a cylinder) an that makes the models fall apart.  The STL file is pretty large for 2beg in ball and stick -- I got 115 Mbytes.  Can probably reduce this by changing Chimera subdivision quality to a lower value (Tools / Viewing Controls / Effects) before saving the STL file.  Another problem is this model has so much detail your printer may not have enough resolution unless it is printed very large (e.g. 20 centimeters long).  Assuming you have a single color printer it might be hard to recognize the hydrogen bonds in the printed model, although they are longer than the covalent bonds.  You could simplify the model by showing only the backbone (Actions / Atoms / Backbone / Full, also "display @H" to get amide hydrogens for hydrogen bonds) or just ribbon plus hydrogen bonds.  Or you could show just 2 of the 5 parallel beta strands to simplify.

	Tom




 


On Jun 17, 2013, at 6:36 AM, Francois Richard  wrote:

> Hi everyone,
> 
> I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer.
> 
> I would like to print the ball and stick representation of the molecule, including the hydrogen bond.
> 
> So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond.
> 
> Do you have any idea how to improve the output?
> 
> Thanks a lot,
> 
> Francois
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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