[Chimera-users] Interactive Chimera demonstrations for teaching

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 24 17:45:45 PDT 2009

In case it may be helpful, here is my general workflow in making the  
Demos distributed with Chimera (in the Tools... Demos menu):

- create a Chimera command script for the whole forward process.  I  
just create it in a text editor and then keep opening it over and  
over after making adjustments.  I find this to be much easier than  
trying to use the Demo Editor at this stage.  Remember to use "wait"  
to prevent overlapping execution of movement commands.  Sometimes  
overlapping execution is OK, but in my experience it sometimes leads  
to different resulting positions on different runs of the same script.

- decide which commands to string together in single lines, separated  
by semicolons (to avoid displaying the intermediate states, since the  
display just gets updated at the end of a line).  This is really done  
in parallel with the above, so I'm still text-editing that Chimera  
command file.

- decide how to chunk it up into panels, then enter these sets of  
commands in the Demo Editor, as well as the accompanying text that  
will show up in the Demo dialog.

- figure out and enter "undo" commands for each panel.  You only have  
to do this if you want the Back button to work.

- add any fancy extras such as links that execute commands (like the  
options to show as sticks or spheres, or show residues from just one  
protein or another in the COX demo).  Sometimes it can be a challenge  
to make sure the "undo" commands will work no matter which of these  
things the user chooses to execute.

I'm sure there are other equally valid but different ways to go about  
this, so feel free to choose your own path!
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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