It certainly does behave as you describe. Our Cytoscape expert (Scooter Morris) is out sick right now and I would need his assistance to determine how to fix the network information/nodes so that the Chimera->Cytoscape coloring works. So unfortunately it will probably be a few days before we can offer any kind of usable fix for this. I'll post something when it's available.

  Eric Pettersen
  UCSF Computer Graphics Lab
  http://www.cgl.ucsf.edu

On Feb 9, 2015, at 6:39 AM, Juan Eiros Zamora <j.eiros-zamora14@imperial.ac.uk> wrote:

Hi all,

I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the structureViz2 plugin.

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

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