iGNM 3-D Visualization Engine

This visualization tool utilizes MDL CHIME for displaying the GNM calculation results in the web browser.  The 2-D plotting tool requires the Java 2 running environment.  You can view two different modes at the same time, plot the modes on a 2-D graph, or connect directly to the PDB, PDBsum, SCOP, or CATH databases using this interface.

If you do not have MDL CHIME installed you can download it for free here.
If you do not have the Java 2 running environment you can download it for free here.

Enter a PDB ID into the form below to begin you Protein Query.

Viewing Mobility Ribbon Diagrams - After entering the PDB ID two CHIME windows will open displaying the ribbon diagrams, Slow mode 1 and Slow mode 2, which describe the residue mobilities in the two slowest modes of motion predicted by the GNM (color code: red-orange-yellow-green-cyan-blue in the order of decreasing mobility). The structures can be rotated/manipulated using the mouse and the CHIME display options accessible by right click on the diagram. The "mode" and "rank" drop-down boxes can be used to view. 

(i) the mobilities of residues for

* slow modes of rank 1 - 20 (rank-ordered by increasing frequency, i.e. slow 1 is the most delocalized/slowest mode)
* fast modes of rank 1 - 20 (rank-ordered by decreasing frequency, i.e. fast 1 is the most localized/fastest mode)
* slow average: average over the two slowest modes
* fast average: average over the ten fastest modes


(ii) the structural elements subject to anticorrelated motions (indicated by red- and blue- colored regions) for

* slow eigenvectors (modes) of rank 1-20
* fast eigenvectors (modes) of rank 1-20

Viewing Plots of different modes - Use the "Plot" button to see a 2-D graph of the mode selected, and the graph will appear in a pop-up window.  Use the "View" drop down menu to scale the graph and focus on a particular section.  Be sure to enter the max and min information into all the appropriate boxes or you may receive an error.  To locate the absolute maximum or minimum points click on the "PDB" button and select "View Max/Min".  You can hold your mouse over a point on the graph to view its exact values. 

An online tool to compare different modes of a given protein or the same mode of different proteins.