[Chimera-users] Chimera help for tomography data!

Tom Goddard goddard at sonic.net
Fri Sep 15 10:35:40 PDT 2017


In brief the command to play through volume planes 0-75 looks like

	volume #0 planes z,0,75

and to record a movie with that you could use

	movie record ; volume #0 planes z,0,75 ; wait 75 ; movie encode ~/Desktop/planes.mp4

Instead of typing in the command line you can put those commands in a file with suffix “.cmd” and open it, helpful when you add more commands.

	Tom

> On Sep 15, 2017, at 9:19 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Sweta,
> If I understand correctly, you have one volume data set and want to play through its planes.  (Volume Series is for when you have multiple 3D data sets.)  It sounds like you are using the slider in the Planes section of Volume Viewer to do it manually.  
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes>
> 
> To do it automatically, as you would want for a movie script, you can use the “volume” command “planes” option:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes>
> 
> There is a nice little example at the bottom of this page… you can click the image to see the short movie and then follow the link to see the script that was used:
> <http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Sep 15, 2017, at 6:19 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan at glasgow.ac.uk> wrote:
>> 
>> Dear All,
>> I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie. 
>> 
>> I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it?
>> 
>> Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated.
>> Thanks and best wishes,
>> Swetha 
> 
> 
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