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

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 9 16:27:43 PST 2015

Hi Juan,
	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

On Feb 9, 2015, at 6:39 AM, Juan Eiros Zamora <j.eiros-zamora14 at 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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