[Chimera-users] volume planes display loop

Thomas Goddard goddard at cgl.ucsf.edu
Mon Oct 27 14:54:59 PDT 2008

Oops!  Forgot to attach the script described in the previous email. 
Here it is.


Tom Goddard wrote:
> Hi Ben,
>   The current Chimera daily builds have a more flexible volume plane 
> cycling interface.  In the planes panel it now has a switch
>   Cycle through [20] planes at speed [30]
> It lets you play through a specified number of planes centered on the 
> currently shown plane.  You start it by clicking a switch and stop it 
> the same way.  There is no control to stop after N planes, and the 
> initial direction of play is the same as when you last stopped playback.
>   There is currently no Chimera command equivalent which would obviously 
> be handy for making movies.  I've attached a Python script which can be 
> used with Chimera commands (example given in script) to control exactly 
> which frames to show in a movie.  Note that the frame rate is only 
> relevant for real-time cycling in Chimera.  Movie recording captures 
> every new frame no matter how slow they are rendered and plays in a 
> movie player at 25 frames per second (adjustable with a movie encode 
> command option).  Chimera movie recording capabilities are very limited 
> now but it is an area we intend to improve.
>     Tom
> Benoit Zuber wrote:
>> Hi,
>> I have got some questions regarding plane display of volumes:
>> Is there a way to cycle through a limited range of planes? For example 
>> if the thickness of my volume is 300, is it possible to cycle from z = 
>> 100 to z = 120, instead of from z = 0 to z = 299?
>> Is there a way to make the cycling through the planes start in the other 
>> direction than when it stopped last time? For example, I click stop 
>> while the display is cycling from low z value to high z value. If I then 
>> click start, the display is going to cycle again from low to high z 
>> value but I would like it to cycle from high to low z value.
>> Is it possible to specify a starting plane and an end plane, and to have 
>> the display going from the starting plane to the end plane only once 
>> (without cycling)?
>> Finally, can all of this be specified through the command line?
>> Cheers,
>> Ben
>> Benoît Zuber
>> MRC Laboratory of Molecular Biology
>> Hills Road
>> Cambridge
>> CB2 0QH
>> United Kingdom
>> +44 1223 402209
>> bzuber at mrc-lmb.cam.ac.uk
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>> Chimera-users at cgl.ucsf.edu
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