[Chimera-users] Selecting specific atoms in MD Movie

Thomas Faour (x2013gua) x2013gua at stfx.ca
Thu Aug 11 16:46:39 PDT 2016

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?



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