[Chimera-users] animation suggestions

Tom Goddard goddard at sonic.net
Fri Feb 18 09:26:16 PST 2011

Hi Matt,

   Those are all good suggestions.  I'll talk to Darren, our animation 
programmer, and perhaps he or I can work on some of them.

   I could see request 2 perhaps being combined with 1.  You could put 
in a pause script command which would then show a dialog that would 
allow you to continue or single step frame by frame from that point on.  
It could single step through any transition, not just reset command 
motions.  It would be limited in that it wouldn't allow backing up, and 
might not allow you to use any other Chimera menu or mouse operation -- 
it would just be frozen, with the options to play a single frame, or to 
resume continuous playback.  The single stepping combined with your 
frame count stamp (request 3) would allow identifying exactly where to 
insert an extra keyframe to avoid a collision between molecules.

   There is a solution for request 5 already.  Of course, you don't want 
to reinstall a bunch of plug-ins not included in the distribution every 
time you update.  To avoid this make a directory, called for example 
chimera-plugins, that is outside of the Chimera distribution directory.  
Install the plugins in that directory and use Favorites / Preferences / 
Category Tools and add the chimera-plugins directory to the Tool 
Locations using the Add... button at the bottom.  Press the Save button 
so that setting is saved in your Chimera preferences.  Installing a new 
Chimera version uses your existing preferences, so all your plugins will 
still work in the new Chimera with no extra fuss.


> 1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could  continue or restart the script.
> 2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2.  Figuring out where&  when kf1.1 should be placed is problematic.  It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command.
> 3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing.
> 4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos.  Having the ability to adjust the diameter of the line is which, which can be done in an obscure way.  Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code.
> 5) I prefer to keep up with the daily builds&  submitting bug reports.  The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers.  Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk.
> thanks for the good product.
> Matthew
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine

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