Hi,

We did some exome sequencing analysis and we have identified some novel mutations that are damaging (according to SIFT predictions) In order to add some protein structure analysis to that work I need to generate contact map of the mutated residues and the active sites around that mutation. I intend to generate the figures which look somewhat like figure b & c in this figure http://www.nature.com/nature/journal/v462/n7274/fig_tab/nature08617_F3.html. I already have generated the structure pdb files using swiss-model. Since I don't have much experience with protein structure analysis I was wondering if somebody can give me pointers as to how I should generate a figure similar to the one given above using either chimera/pymol.

regards