Contact Map in VMD ?

11 November 2017 1 1K Report

I want to obtain contact map in VMD for finding helix-helix interaction in my Dimer simulation. I know that I can use VMD to do this via: Extension->Analysis->Contact Map, but how to select the two helices for obtaining contact map ? I got nothing when I just opened contact map through extension after loading the structure and the trajectory.

Martin Klvana

Step 4: "In the left hand column, select molecule numbers for Molecule A and Molecule B. Select the parts of the molecules which you wish to compare." http://www.ks.uiuc.edu/Research/vmd/plugins/contactmap/

To select a helix composed of residues 1 to 10: resid 1 to 10 http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html

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