[Chimera-users] pause during a fly-by?

Elaine Meng meng at cgl.ucsf.edu
Sat Aug 22 11:07:33 PDT 2009

Hi Daniel,
You might consider writing your script with a series of "reset"  
commands rather than "fly" -- the difference is that fly considers  
the trajectory to be taken after the next position, so that the whole  
thing looks smoother.  If A,B,C,D are saved positions, schematically:

fly A -> B -> C -> D
where the approach to C is already being considered before arriving  
at B, versus

reset -> A; wait
reset -> B; wait
where each reset command can specify number of frames (does not have  
to be instantaneous)

The wait commands prevent the movement commands from overlapping  

Shift-Esc will pause the script after the current command is done.   
If it is in the middle of a reset to C, it will go that far and then  
stop at C.  Then it can be resumed with another Shift-Esc. That is  
not as precise as what you had asked about (instantaneously pausing),  
but more precise than after an entire fly command finishes.

A demo is inherently a series of commands, and doesn't allow pausing  
in the middle of a command, so "reset" is probably also needed in  
that case.  It is the only way I can think of in Chimera where you  
can just press a button to go back to a previous state.  Easy for the  
user, but...

Demo issues:
- you would need to start the demo by opening a session with your  
saved positions, unless you
know how to generate those positions by a series of commands
- the "go back" feature automatically takes care of positions, but  
the demo creator is responsible for figuring out any other commands  
needed to revert to the previous state (any displaying/undisplaying,  
changing colors, styles).  It can be more confusing than it sounds!

You can see the "guts" of a demo by choosing it from the Tools...  
Demos menu (starting to play it back) but then choosing "File... Open  
in Editor" from the demo panel.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 21, 2009, at 6:25 PM, Tom Goddard wrote:

> 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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