[Chimera-users] presets, python and printing

Thomas Goddard goddard at cgl.ucsf.edu
Mon May 10 10:45:20 PDT 2010

Hi Dan,

   I don't know if anyone has used Chimera for export to a Z-corp 
printer.  The part I'd wonder about is how the color information is 
encoded.  STL format does not include color info, although there are 
some hacks to the format that provide it


Chimera does not support color in STL currently.

   It would be pretty easy to make some kinds of customizations to the 
Chimera interface.  For instance all, the current menus could easily be 
eliminated and one new menu added with just the 6 things you want to 
provide access to (open, save, quit, color, ...).  This would be done by 
commenting out various lines in chimera/share/chimera/tkgui.py where 
those menus are placed in the menu-bar (on Mac the file is 
Chimera.app/Contents/Resources/share/chimera/tkgui.py) and adding your 
own menu.

   Yeah, a general undo has to be designed into the software from the 
beginning.  Chimera has some specialized undo capabilities (undo motion, 
undo selection).  If you know the steps in your work-flow where undo is 
really important it may be possible to add that kind of special undo. 
Auto-save is not available but would be pretty easy -- but may be 
annoying as a session save could take 10 seconds depending on data size.


> Hello everyone,
> My colleague and I are planning to incorporate 3D physical models into
> the introductory biochemistry course at our university, and I want
> students to use Chimera in the design of models. I've seen the technotes
> on 3D models made by the uPrint printer
> (http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html). We'll
> hopefully be collaborating with the folks at MSOE on this, using their
> Z-corporation printer. They use RasMol to design models, but the file
> read by the printer is in .stl format.
> Here are my questions:
> 1) Has anyone used Chimera to create models to be printed on a Z-corp
> printer? (if yes, I'll have many more questions for you...)
> 2) Is it possible to define a user preset in Chimera with Python? I know
> this isn't currently possible with chimera commands, and I am *just*
> getting into Python now. Because students have difficulty jumping in to
> a project like this if they first have to learn to enter commands at a
> prompt, I want to make some presets that apply settings compatible with
> a 3D model; bond thickness, colors, etc.
> 3)If one knew Python, would it be possible to design a simplified user
> interface for Chimera? Even as simple as a pop-up window that contained
> the key features I want students to have access to right away?
> 4) Probably the biggest drawback to using Chimera with undergrads is the
> lack of an "Undo" button.  I'm guessing this is extremely difficult to
> implement because of all 3rd party extensions incorporated into Chimera?
> What about an option to autosave every five or ten minutes?
> Thanks
> Dan
> --
> ____________________________
> Daniel Gurnon, Ph. D.
> Assistant Professor of Chemistry
> DePauw University
> Greencastle, IN 46135
> p: 765-658-6279
> e: danielgurnon at depauw.edu <mailto:danielgurnon at depauw.edu>
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