[Chimera-users] Chimera help for tomography data!

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 20 09:36:02 PDT 2017


Hi Swetha,
Fitting the structure and then making it appear/disappear using your movie script can be considered two separate issues.  

You could have the fitted structure saved in a session, so you only do that once.  Then you can restore the session and run the movie script, which could include commands to hide/show the model interspersed with planes playback commands.  For hide/show, see “modeldisplay” “display” and “ribbon” commands.  See command documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

Fitting can be done with the Fit in Map GUI (menu: Tools… Volume Data… Fit in Map) or the “fitmap” command, although the latter includes some additional options not in the GUI, like global search or sequential or symmetrical fitting of multiple subunits.  In most cases, the automated fitting is combined with manually (with the mouse) repositioning one model relative to the other.  Once the fit is to your liking, then save the session for use with your movie script.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>

Moving models by hand:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html>

We wouldn’t be able to comment on the recording error unless you provide more details.

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 20, 2017, at 3:14 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan at glasgow.ac.uk> wrote:

> 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.
> 
> Thanks,
> Swetha
> 



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