Max-Planck-Institut für Informatik
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RINalyzer Tutorials

Tutorials for Cytoscape 3.x

Tutorials for Cytoscape 2.x

In the following, screenshots for each step appear when hovering the mouse over (image). If you cannot see the whole image, you can use the keyboard arrows to move to the right or to the bottom while holding the mouse over the image.

In this tutorial, it is assumed that you have followed the steps described in Tutorial 1, i.e. the Cytoscape session pdb1hiv_h.cys is opened and the corresponding 3D structure is loaded in Chimera.

Download ConSurf-DB data

  • Go to our RIN data download page.
  • Enter the PDB identifier 1hiv in the search form (image) and click the Search for RIN data button.
  • Besides the RIN data for 1hiv, you can download two node attribute files with residue conservation data (image).
  • Click on the first link (image) and save the file to your local file system (image) under the name (image).
  • Click on the second link (image) and save the file to your local file system (image) under the name (image).

Load data into Cytoscape

  • Switch to Cytoscape
  • Import the node attribute files and by performing the same steps for each file:
    • Go to FileImportNode Attributes... (image)
    • Select the node attribute file in the file browser and click on the Open button (image).
    • Close the dialog informing you about the successfully performed action (image).

Map residue conservation to node/residue colors

  • In the Control Panel, go to VizMapper (image).
  • Go to the Node Color row (image), click on the right field to change the attribute to ResidueConsurfColor (image) and change the mapping type to Discrete Mapping (image).
  • The ConSurf-DB color scale uses 9 values to represent the conservation scores (9 - conserved, 1 - variable). Therefore, there are 9 rows with values to be mapped to colors (image). You can set color for each value by clicking on the right field in the row (image) and then on the ... button.
  • Set the colors as in this image.
  • Color residues in Chimera according to the node colors in the network view. Go to PluginsRINalyzerProtein StructureSync 3D view colors (image).
  • The network and the 3D structure should look as in this image.