[Chimera-users] Issue with cytoscape plugin

Juan Eiros Zamora j.eiros-zamora14 at imperial.ac.uk
Tue Jun 23 13:17:07 PDT 2015


Hi Chimera users,

I'm using cytoscape and structureviz to visualize interaction networks 
of my MD simulations. I've been using it for quite awhile now on the 
normal structure of my protein. Now I am simulating it with two adjacent 
phosphorylated serines (all is done with AMBER), and I think there are 
some issues with this because:

1) If I select a region of the protein that does not contain this 
"special" aminoacids, the RIN visualization works just fine

2) When I select the region that contains these two phosphorylated 
Serines (about +-10 aminoacids from them), when the RIN is set up on 
cytoscape I get the following error:

    RINLayout
   Fetching coordinates from Chimera...
   null

Which is pretty generic. What is more confusing is that if I select all 
the system (which is not interesting for me, but I've done it anyway to 
try) it seems to work as well.

My cytoscape version is 3.2.0 and all the apps in it are up to date:
     structureViz2 1.0.1
     RINalyzer 2.0.0

I think the RIN is being calculated just fine, but it's having problems 
recognising the 3D shape in Chimera. Also, it fails to synchronize the 
colours, I don't know if this is related to what I'm reporting here, but 
I suspect it is.

Does anyone know how can I proceed? It would be very useful for me to 
compare the RINS of the non-phosphorylated version of my system to the 
phosphorylated version.

Thanks for any help,

Juan Eiros



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