[Chimera-users] Interactive Chimera demonstrations for teaching

Tom Goddard goddard at cgl.ucsf.edu
Mon Aug 24 11:49:34 PDT 2009

Hi Dan,

  If you haven't already, you should check out the two demos (cox 
inhibitors, hormone-receptor complex) in the Chimera Tools / Demos 
menu.  These were made by Elaine Meng.  If you look at pane 7 of the cox 
demo there are some html-style links "sticks" and "spheres" that allow 
you to change rendering options.  You can also use the normal Chimera 
menus and tinker with the rendering and view point and the demo will 
usually revert to the normal depiction when you go to the next pane.  
Whether it does or not depends on how thorough the commands that define 
the demo are about setting all the display styles in case the user has 
fiddled.  Going from panes 4 to 5 there is some motion of the 
molecules.  But then pressing the back button jumps immediately to the 
preceding positions -- it does not show the motion in reverse.  It may 
be easy to make the back button reverse the motion.  In general the back 
operation has to be given as a series of commands that the demo creator 
knows will undo the forward step.  You could put in the backwards motion 
commands.  I have never made a demo so I am guessing.

  We are interested in improving Chimera for interactive teaching.  Our 
thinking when developing the demo editor was more geared towards showing 
a researcher new to Chimera some of the Chimera capabilities.  Creating 
these demos does not require programming knowledge, but rather a good 
knowledge of the Chimera commands.


Before you team up with some computer science people, I think the steps 
should be: 1) study the two demos included in Chimera, and the commands 
used in those demos, 2) try making a simple demo from your own material, 
3) talk with us about the problems you find.  I think you'll encounter 
two problems, first that some needed commands don't exist, and second 
that the demo editor and player are clunky (it hasn't been used much to 
our knowledge).  Both of these things we can work with you to improve -- 
possibly with pretty quick turn-around time (days/weeks).


-------- Original Message --------
Subject: Re: [Chimera-users] pause during a fly-by?
From: Daniel Gurnon
To: goddard at cgl.ucsf.edu
Date: 8/22/09 9:24 AM
> Thanks Tom. I'll try making some demos. From the ones I've seen, rewinding the demo is more like "reset", i.e., any motion won't be reversed but instead the model(s) will be reset to their position and rendering from the previous step. But it should provide much of what I need. 
> Over the past few months, I've been learning Autodesk Maya and talking with Gael McGill and some of the others out there that do molecular animation. While I think animation software like Maya can be a very powerful teaching tool (especially when you need to model things for which there is no 3D data set), the finished movies lack interactivity. Ideally I want modules that automate some of the learning experience (fetching a structure, rendering to highlight appropriate features, taking the viewer on a fly-by tour of the system) while also leaving the participant free to pause and explore the scene on their own. The demos in Chimera are pretty close to what I want actually, but there are a few things I'd change if I could...motion rewinding is one, but it would also be useful to add buttons enabling the user to change rendering options at each demo stop-point without the risk of screwing up the rest of the demo. It would also be nice to instantly reset the demo to the current point if you made a change you want to undo. In a nutshell, I want to design modules that any student or any teacher could use with minimal time invested in learning Chimera.  I really think Chimera has a lot of potential for teaching, but the learning curve associated with the program makes it tough for the inexperienced to get the most out of the Chimera's interactive capabilities.
> Do you think it would be feasible (and a good idea) for me to team up with some computer scientists at my school and work on retooling the demo editor with the goal of designing several student-friendly, interactive modules? I have a lot of experience with teaching, but none with programming, so I know what I want...I just don't know if it's possible.  Any advice you can offer is much appreciated!
> Dan

-------- Original Message --------
Subject: Re: [Chimera-users] pause during a fly-by?
From: Tom Goddard <goddard at cgl.ucsf.edu>
To: Daniel Gurnon
Date: 8/21/09 6:25 PM
> Hi Daniel,
>   The demo capability in Chimera is designed to do what you want 
> including rewind.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html
> It doesn't allow pausing in the middle of a motion -- only between 
> panels (maybe between individual commands associated with a panel - not 
> sure).  But the idea is that the duration of motion in each panel would 
> be short.  We haven't made many demos and this tool may be pretty rough 
> around the edges.
>   The trouble with the pause command or Shift-Escape to pause/resume a 
> script is that the fly command returns immediately after you invoke it.  
> It sets up playing the motion which then happens after the command 
> returns.  Normally that motion could be halted with the command 
> "freeze".  This works with other motion commands "reset", "roll", 
> "move", and it should work with "fly" but doesn't yet work for "fly".  
> In any case, it simply terminates the motion and there is no way to 
> restart it, so that won't do what you want.  There is no mechanism to 
> pause the playback in these motion commands, though maybe "pause" and 
> the Shift-Escape key should be made to do that.  Currently those 
> mechanisms just block running of additional commands I believe.
>   I wonder whether pause/resume would be adequate for teaching 
> purposes.  Seems very likely to me that you will need rewind.  By the 
> time a student asks a question the motion is already past the relevant 
> section.  We don't have any rewind capability in the motion commands or 
> in general scripts, only the demo tool, and even there I think can be 
> tricky to make it work.
>     Tom
> -------- Original Message --------
> Subject: [Chimera-users] pause during a fly-by?
> From: Daniel Gurnon
> To: chimera-users at cgl.ucsf.edu
> Date: 8/21/09 5:52 PM
>> Hi all,
>> I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone,  and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in?
>> Thanks
>> Dan
>> ____________________________
>> Daniel Gurnon, Ph. D.
>> Assistant Professor of Chemistry
>> DePauw University
>> Greencastle, IN 46135

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