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)

The first column of a match means the color code from the ligand atom and the second column means the color code from the corresponding 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).

#####################################################
#                             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