I use structureviz  to open chimera through cytoscape and load an MD trajectory of a protein to create a RIN through Analysis --> Residue interaction network...

What I am trying to do is colour the nodes in cytoscape based on which chain they belong to. My protein has three chains, and in chimera I color each differently. In cytoscape, I go to apps --> structureviz--> synchronize residue colors. Here I am given two options. The first one is “Apply colors from current network view to associated Chimera models”: This one works fine, but it is not what I want. What I want to do is the second option: “Apply colors from associated Chimera models to current network view”, but when I clik on OK it does nothing.

Anybody having the same problem or some suggestions on how I might solve this?

Much appreciated,

Juan Eiros