[Chimera-users] Create an artificial bond between ribbons for 3D printing

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 28 08:57:06 PDT 2015


Dear David,
You can show pseudobonds as “stick” instead of lines.  There are several routes; one way is to select the pseudobond(s) and then use the Selection Inspector: Ctrl-click on one, then up arrow to select all of them if there’s more than one, then click the green magnifying glass icon near the bottom right corner of the Chimera window.  In the Selection Inspector, Inspect: Pseudobond, change bond style to stick.  You can also edit the “radius” value.

Another way is to use the “setattr” (set attribute) command:

setattr p drawMode 1
setattr p radius .5

(you can find out the attribute names to use in this command by mousing over the corresponding settings in the Selection Inspector)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

There is also a “struts” command to automatically place strengthening pseudobonds and thicken the ribbons to make models more robust for 3D printing:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html>

However, your approach of manually creating pseudobonds may also be effective.  Besides using distance measurements, you can create a series of pseudobonds by listing the atom pairs in a text file and reading it in with Pseudobond Reader:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 28, 2015, at 6:47 AM, David Bhella <David.Bhella at glasgow.ac.uk> wrote:
> 
> Dear Chimera users,
> I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part.
> So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long.
> 
> The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported.
> Any suggestions would be gratefully received.
> Thanks,
> D.




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