Coloring and Subcluster Matching: Difference between revisions

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  cp /your receptor preparation folders/xtal-lig.pdb .
  cp /your receptor preparation folders/xtal-lig.pdb .
  cp /your receptor preparation folders/working/rec.crg.pdb .
  cp /your receptor preparation folders/working/rec.crg.pdb .
cd dockfiles
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb


For coloring your matching sphere, you must have
=== 1.2 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"

Revision as of 18:50, 31 March 2021

Written by Jiankun Lyu on March 31st, 2021.

1. Generate colored matching spheres

1.1 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

1.2 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"