[Chimera-users] presets, python and printing

Elaine Meng meng at cgl.ucsf.edu
Mon May 10 09:41:29 PDT 2010

Hi Daniel,
I'll partly address your question #2, user presets, and leave the  
other questions for others to address.

I don't know python, but something very similar can be done with the  
alias command.  You can create rather elaborate "action" (start-of- 
line) aliases, and the alias definition can include several Chimera  
commands concatenated with semicolons.  In Chimera 1.5, such aliases  
will then be listed in an Aliases menu in Chimera, and you only need  
to choose from the menu to execute them.

For example (this should be all one line although the annoying mail  
program will probably break it up):

alias ^preset_nuc set bg_color tan;set subdivision 2;~set  
silhouette;nuc side fill orient false;nuc ndbcolor


You could supply students with a Chimera command file setting up  
several of these aliases.  They would only need to open the file once  
to set up all the aliases, since they are saved in the preferences  
file.  Or, if there is some kind of computer lab where you have  
control over the installation, you could set this up yourself  
beforehand.  Example files to test the above alias: 1ehz (RNA), 1d86  

You would probably want to include explicit background color,  
silhouette and subdivision settings as in the above example, since the  
publication presets may set these to values that are not optimal for  
interactive use.

Limitations to this approach:
(A) requires Chimera version 1.5 (daily build) if you want the Aliases  
menu; in older versions, the alias can still be used, but just as a  

(B) can only incorporate things that can be done with Chimera commands  
(although we have been steadily improving on this front -- see  
especially "set" and "setattr" for global settings and model/residue/ 
atom attribute settings, respectively.  A good way to adjust stick  
thickness is by changing the model attribute stickScale, e.g.: setattr  
m stickScale 0.5 )


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

On May 9, 2010, at 7:51 AM, Daniel Gurnon wrote:

> 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

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