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

#####################################################
#                             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 you point to the colored matching spheres

##################################################### 
## INPUT FILES / THINGS THAT CHANGE
receptor_sphere_file          ../dockfiles/matching_spheres.cl.sph