[Chimera-users] Chimera help for tomography data!

Swetha Vijayakrishnan Swetha.Vijayakrishnan at glasgow.ac.uk
Thu Oct 5 08:35:47 PDT 2017

Hi Elaine,

Thanks for this input. I did manage to fit the models into the tomogram and use the model display as well.

However i was trying to clip some of the fit structural models to show the interior which at the moment i am struggling with using clip or the mclip options. Any advice on this from you will be greatly appreciated.

Also i was trying to save the chimera session to get back to another time, but i seem to be getting an error msg saying one of the volumes has not been saved, i.e. the original tomogram that was rescaled and inverted using the volume filter/scale options and that appears as a new model now in my volume viewer. I tried using the "save map” option selecting this model and naming it as .mrc in the volume viewer menu prior to resaving the session but i am still unable to do so and keep getting the same error (see attached below). How do i solve this problem?

Thanks and Best,


[cid:FB049C5C-AD56-4384-BC8F-5CB6CC23A586 at campus.gla.ac.uk]

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 20 Sep 2017, at 17:36, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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:

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.

Moving models by hand:

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

I hope this helps,
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<mailto: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.


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