[Chimera-users] Issue with cytoscape plugin
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.
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:
> Fetching coordinates from Chimera...
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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