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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.

Load RIN data into Cytoscape (automatically)

In this step, it is assumed that you have chosen a protein of interest with an experimentally determined 3D structure and you know the PDB identifier of this protein. In this example, we will use the PDB entry 1hiv, an HIV-1 protease.

  • Launch Cytoscape
  • Go to FileImportNetworkPublic Databases... (image).
  • In the Data source drop-down menu, choose the RINdata Web Service Client (image).
  • Enter a PDB identifier in the search form (image).
  • If UCSF Chimera is not installed in the default location and it is your first time to use this service, enter the path to the UCSF Chimera executable (image).
  • Click the Retrieve RIN data button to automatically retrieve the archive file, which contains the RIN data generated for the target PDB identifier 1hiv:
    • a PDB file with the 3D protein structure from the original PDB file (as downloaded from the PDB) with hydrogens added (pdb1hiv_h.ent);
    • a SIF file containing the residue interaction network for all chains in the PDB file (pdb1hiv_h.sif);
    • an edge attribute file with double edge weights reflecting the strength of interactions between residues (pdb1hiv_h_intsc.ea);
    • an edge attribute file with integer edge weights representing the number of interactions between residues (pdb1hiv_h_nrint.ea).
  • The network and edge attribute files are loaded automatically. The structure file is saved to USER_HOME/CytoscapeConfigureation/pdbs/ and opened in UCSF Chimera. The default visual properties and the RIN layout are applied automatically. Your screen should look as in this image.
  • If you are do not want to import other RINs, close the dialog using the X button in the upper right corner (image).

Load RIN data into Cytoscape (manually)

  • Import the network file pdb1hiv_h.sif:
    • Go to AppsRINalyzerImport RIN from file (image)
    • Click the Open a File... button (image).
    • Go to the 1hiv directory that contains the RIN files. Select the file pdb1hiv_h.sif in the file browser and click on the Open button (image).
    • Enter "pdb1hiv_h.ent" for the name of the structure associated with this RIN (image).
    • Click the OK button to load the data into Cytoscape. Your screen should look as in this image.
  • Load the PDB structure file pdb1hiv_h.ent:
    • If UCSF Chimera is not installed in the default location and it is the first time to launch it, go to AppsstructureVizSettings... (image) and enter the path to the UCSF Chimera executable at the bottom of the dialog (image). Click OK to save the settings.
    • Go to AppsRINalyzerOpen Structure from File (image).
    • Select the PDB file in the file browser and click on the Open button (image).
    • It may take a while until UCSF Chimera is launched and the 3D structure is opened. Your screen should look as in this image.
  • Import the edge attribute files pdb1hiv_h_intsc.ea and pdb1hiv_h_nrint.ea by performing the same steps for each file:
    • Go to FileImportTableFile... (image)
    • Select the edge attribute file in the file browser and click on the Open button (image).
    • In the Import Columns from Table dialog, choose Edge Table Columns in the Import Data as drop-down list, check the Show Text File Import Options checkbox, choose the option Other and enter = for Delimiter, check the option Transfer first line as column names (image).
    • To set the column names, right-click the column names and enter the new names, ID for the first column (image), InteractionScore for the second (image).
    • In everything looks as in this image, click OK to complete the import.

Adapt and enrich the views

  • Show all graphics details in the network view, as they are not displayed in a zoomed-out view. Go to ViewShow Graphics Details (image).
  • Annotate the RIN with structural properties:
    • Go to AppsRINalyzerAnnotate RIN from Chimera (image).
    • Select one or all (by clicking Ctrl + A) residue attributes to be transferred as node attributes (image).
  • Synchronize the colors:
    • Go to AppsRINalyzerSync RIN colors with Chimera (image).
    • Choose the first option to transfer the colors of the nodes to the residues (image).
    • Your screen should look as in this image.
  • Rotate the 3D structure and to layout the network according to the 3D view, go to LayoutRINLayout (image). In order to see the whole network click on the 1:1 (image) icon in the Cytoscape toolbar.
  • Adapt the visual settings of the RIN:
    • Go to AppsRINalyzerRIN Visual Properties (image).
    • In the General & Nodes tab you can choose how the node label should be displayed. For example, if you can select only residue number and type (image), you will observe that the node labels are updated.
    • In the Edges tab, you can choose which edge types should be displayed. The network view is updated automatically each time you check or uncheck an edge type box.
    • You can add backbone edges by checking the box on the top of the dialog (image).
    • In the Edges tab, you can enable/disable the option Straighten edge lines if you do (not) want multiple edges to be drawn as straight parallel lines as in this image.
    • You can change the value of each other property and you will see the resulting network view by clicking the Apply button. More details about the different options can be found here.
    • If you are satisfied with the view of your RIN, apply the changes by clicking the Apply button and close the dialog with the Close button.
  • Store the current network, the loaded attributes and the current network view into a Cytoscape session file called pdb1hiv_h.cys. The session file can be opened again anytime.
    • Go to FileSave (image).
    • Enter the session file name pdb1hiv_h.cys into the file browser and click on the Save button (image).