[Chimera-users] Chimera help for tomography data!

Swetha Vijayakrishnan Swetha.Vijayakrishnan at glasgow.ac.uk
Wed Sep 20 03:14:52 PDT 2017

Thank you Elaine and Tom. That was very useful although i seem to have some trouble encoding the movie. It throws up a Python error that could be a version problem. I shall update to the latest version and check again.

The other question i had was how do i fit a model onto the tomogram volume, specifically a 3D structure obtained from subtomogram averaging? Is this possible in the current latest version of chimera? Ideally i would like the planes of the tomogram volume to move through one way and the 3D structure coming up as it moves up the other way.



Dr Swetha Vijayakrishnan

MRC-University of Glasgow Centre for Virus Research (CVR)
University of Glasgow,
Sir Michael Stoker Building,
464 Bearsden Road,
Garscube campus
Glasgow G61 1QH

Email: Swetha.Vijayakrishnan at glasgow.ac.uk<mailto:Swetha.Vijayakrishnan at glasgow.ac.uk>
Phone: +44 (0) 141 330 4025

On 15 Sep 2017, at 18:35, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

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.


On Sep 15, 2017, at 9:19 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto: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.

To do it automatically, as you would want for a movie script, you can use the “volume” command “planes” option:

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:

I hope this helps,
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<mailto: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,

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