[Chimera-users] What happened to my model?

Sara Cuellar mealynncuellar44 at gmail.com
Wed Jun 17 12:03:10 PDT 2015

Thank you so much! I was able to modify the protein completely through
Chimera and now its waiting to be printed.

On Wed, Jun 17, 2015 at 11:53 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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