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
Hi Juan Eiros, Can you send me an example file? That will help me debug this. Thanks! -- 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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participants (2)
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Juan Eiros Zamora -
Scooter Morris