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 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> 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 (DNA) 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 command (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 ) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.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 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