[Chimera-users] Problem using structureViz plugin for Cytoscape - Chimera

Juan Eiros Zamora j.eiros-zamora14 at imperial.ac.uk
Mon Feb 9 06:39:03 PST 2015

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 

Much appreciated,

Juan Eiros

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