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How to depict edges as an indicator of no. of frames in which two residue interact in Residue interaction network using Cytoscape?

I am using RIP-MD tool to generate Residue interaction network from MD trajectories. the tool generates GML files which I load in Cytoscape. I want to visualise network in such a way that edge weight denotes the number of frames (percentage of total frames of MD trajectories) in which two residues interact. The edge weight may be denoted as thickness of edge or change of colour. I want edges to denote the number of times interaction between residue occurs in different frame of MD trajectories. Please let me know how can I achieve that?

rip-md rin md-simulation cytoscape
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updated by Jean-Karim Heriche Jean-Karim Heriche • written by Anjali • Anjali

1 answer

You need to apply a style to the edges. Check the styles docs and in particular tutorial 2 which shows how to apply style to edges.

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written by Jean-Karim Heriche Jean-Karim Heriche

Thank you Jean for suggesting this. However when I am trying these options I don't get the option to change stroke color or width on the basis of frequency of residue interaction. That is my main concern edges to depict frequency of residue interaction in different MD trajectory frames.

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written by Anjali • Anjali

Please use the ADD COMMENT or ADD REPLY buttons associated with the post you want to reply to. This keeps the discussion organized.

You need to have the frequency of residue interaction as an edge attribute so that it appears in the available data column field.

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written by Jean-Karim Heriche Jean-Karim Heriche

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