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@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