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

[Elaine Meng]

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  
execution.

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
-----
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
                       http://www.cgl.ucsf.edu/home/meng/index.html

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
>>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users