[Chimera-users] volume planes display loop
bzuber at mrc-lmb.cam.ac.uk
Tue Oct 28 08:13:41 PDT 2008
Thanks very much Tom, it works fine!
In this case, I understand that opening the script a second time stops
In a more general case, once a script has started, how can I interrupt
it before it ends?
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 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  planes at speed 
> > 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
> >> _______________________________________________
> >> Chimera-users mailing list
> >> Chimera-users at cgl.ucsf.edu
> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 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.
> # p.axis.set(p.axis_names) # 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.
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