[Chimera-users] Selecting specific atoms in MD Movie

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 12 10:48:55 PDT 2016

Hi Thomas,
It’s difficult to answer questions like this without the data… I only have one low-confidence guess, which is to try  :52.water instead of :52  

…as mentioned in the “subcategories” section of

If that doesn’t work, you would have to send us the data (or a smaller sample, if possible).  You could send it to just me if you don’t want to send to the whole list.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 11, 2016, at 4:46 PM, Thomas Faour (x2013gua) <x2013gua at stfx.ca> wrote:

> Hello there,
> I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered “liquid”, “hexagonal ice” or “cubic ice”. So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly.
> I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands:
> colour blue,a :52
> select :52
> in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command:
> color blue,a @OW
> however does work. I am currently using XTC trajectories, in case that is relevant. 
> What might fix my problem? Or is there a better way I could be doing this?
> Cheers,
> Thomas

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