Coloring and Subcluster Matching
Written by Jiankun Lyu on March 31st, 2021.
Generate colored matching spheres
Create a directory and copy necessary files from your original receptor preparation folders
set workdir = /where you want to run your coloring and subcluster matching/
mkdir -p ${workdir}
cd ${workdir}
cp /your receptor preparation folders/dockfiles . -r
cp /your receptor preparation folders/INDOCK INDOCK_ori
cp /your receptor preparation folders/xtal-lig.pdb .
cp /your receptor preparation folders/working/rec.crg.pdb .
cd dockfiles
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb
Generate colored matching spheres
cd ../ /nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb" cp matching_spheres.cl.sph ../dockfiles
The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.
Prepare your INDOCK file for color matching
The color codes for matching spheres
positive (1) negative (2) acceptor (3) donor (4) ester_o (5) amide_o (6) neutral (7) not_neutral (8) positive_or_donor (9) negative_or_acceptor (10) neutral_or_acceptor_or_donor (11) donacc (12) positive_or_acceptor (13) negative_or_donor (14) negative_or_acceptor_or_donor (15) positive_or_acceptor_or_donor (16)
The color codes for atoms in the rigid fragment in db2 files
positive (1) negative (2) acceptor (3) donor (4) ester_o (5) amide_o (6) neutral (7)
A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).
Add the section below into your INDOCK file
##################################################### # COLORING chemical_matching yes case_sensitive no match 1 1 match 2 2 match 3 3 match 4 4 match 5 5 match 6 6 match 7 7 match 1 8 match 2 8 match 3 8 match 4 8 match 5 8 match 6 8 match 1 9 match 4 9 match 2 10 match 3 10 match 7 11 match 3 11 match 4 11 match 3 12 match 4 12 match 1 13 match 3 13 match 2 14 match 4 14 match 2 15 match 3 15 match 4 15 match 1 16 match 3 16 match 4 16 #####################################################
Make sure your INDOCK parameter points to the colored matching spheres
##################################################### ## INPUT FILES / THINGS THAT CHANGE receptor_sphere_file ../dockfiles/matching_spheres.cl.sph