[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
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

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.
Best,
Elaine
-----
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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