[Chimera-users] What happened to my model?

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 17 10:53:44 PDT 2015


Hi Sara,
It can be difficult to pinpoint issues when mutliple programs are involved, since we only know the details of our program.  Sometimes other programs have problems that interact in ways that we don’t know about, for example, problems reading files from Chimera.   However, here’s one idea:

It sounds like you exported VRML from Jmol and then used Chimera to convert the VRML to STL.  Even though it still looked OK, our VRML display is relatively simple and it might work better to go from the original format (PDB, I guess) to STL in Chimera.  In Chimera, you could open the PDB and easily hide or delete all but chain A, change the display style, and export as STL.  For example, commands:

~ribbon
~display
display :.A at CA
setattr m stickScale 5

You can show the Chimera command line from the Favorites menu.  Bigger stickScale gives fatter CA-trace sticks. Then export as STL and see if it looks better. 

Chimera export limitations:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>

Chimera has a “struts” command to strengthen structures for 3D printing: 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.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 Jun 17, 2015, at 7:40 AM, Sara Cuellar <mealynncuellar44 at gmail.com> wrote:

> So, in my line of work we are focusing on the protein Dihydrofolate Reductase. Using Jmol, I was able to remove all chains except for chain A, and also increased the diameter of the backbone so that it may be printed. When I opened it in Chimera to export it from VRML file to an STL file, it still looked fine. However, when it was opened in my 3d printing program, parts of the protein were missing. All I see is floating fragments. Is there any way I can fix this using chimera? I have included images of the protein.
> <brokenDHFR.png><DHFR in Chimera.png>



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