[Chimera-users] volume planes display loop

[Tom Goddard]

Hi Ben,

  There is no mechanism for stopping a Chimera script (python or 
commands) in the middle.  The planes.py script I gave you quickly 
finishes and the cycling through the planes is handled by the volume 
dialog which uses a timer to periodically update the plane being 
displayed.  Running the script a second time tells the volume dialog to 
cancel that timer. 

    Tom


Benoit Zuber wrote:
> Thanks very much Tom, it works fine!
> In this case, I understand that opening the script a second time stops
> the loop.
>
> In a more general case, once a script has started, how can I interrupt
> it before it ends?
>
> Cheers,
> Ben
> On Mon, 2008-10-27 at 14:54 -0700, Thomas Goddard wrote:
>   
>> Oops!  Forgot to attach the script described in the previous email. 
>> Here it is.
>>
>> 	Tom
>>
>>
>> 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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>>>>   
>>>>         
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>>>       
>> plain text document attachment (planes.py)
>> # -----------------------------------------------------------------------------
>> # Start or stop volume plane display.  Useful for making a movie that steps
>> # through data planes.  Example Chimera command sequence to make movie
>> # showing 10 planes starting at plane 47 of a 2048x2048x100 data set.
>> #
>> #   volume #0 region 0,0,47,2047,2047,47
>> #   cd /location/of/planes/script
>> #   movie record supersample 3
>> #   open planes.py ; wait 10 ; open planes.py
>> #   movie stop
>> #   movie encode output planes.mov
>> #
>> from VolumeViewer.volumedialog import volume_dialog
>> p = volume_dialog().plane_panel
>> if p.cycle_planes.get():
>>     p.cycle_planes.set(False)       # Stop playback.
>> else:
>> #    p.axis.set(p.axis_names[2])         # Set plane axis 0 is x, 1 is y, 2 is z
>> #    p.plane.set(50)                     # Set starting plane number (0,1,2...)
>>     p.play_direction = 1                # Forward.  Use -1 for backward play.
>>     p.cycle_planes_count.set(100000)    # Reverse direction after N planes.
>>     p.cycle_frame_rate.set(30)          # Maximum frames per second.
>>     p.cycle_planes.set(True)            # Start playback.
>>     
>
>