Coloring and Subcluster Matching: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
Written by Jiankun Lyu on March 31st, 2021. | 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/ | set workdir = /where you want to run your coloring and subcluster matching/ | ||
| Line 15: | Line 15: | ||
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb | $DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb | ||
=== | === Generate colored matching spheres === | ||
cd ../ | cd ../ | ||
| Line 21: | Line 21: | ||
=== | === Prepare your INDOCK file for color matching === | ||
Revision as of 18:54, 31 March 2021
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"