[Chimera-users] Issue with cytoscape plugin

Scooter Morris scooter at cgl.ucsf.edu
Tue Jun 23 14:42:06 PDT 2015

Hi Juan Eiros,
     Can you send me an example file?  That will help me debug this.


-- scooter

On 06/23/2015 01:17 PM, Juan Eiros Zamora wrote:
> 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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