It is difficult to determine how a 2D amino acid sequence threads through the 3D cryo-EM image without a template. Many different applications have been created to improve this process. Recently a software tool known as RaptorX has been created to understand local contacts on an amino acid sequence. In order to explore how this information can be utilized, I wanted to color code amion acids in the 3D image. This program uses the contact predictions and displays the results on a 3D image of the protein.

First open Chimera

Open the protein that you would like to see the contacts. Download the contact map and delete everything in the file except the contacts. Replace all spaces with commas in the contact map file.

There are 4 parameters, the location of the script, the location of the contact map, whether the script should recolor residues (0 for no 1 for yes), the lowest confidence interval the script should use.

EX: run C:\Users\dhaslam\Desktop\contactColorer.py "C:/Users/dhaslam/Downloads/274635.all_in_one/274635.all_in_one/274635.contactmap.txt" 0 .8