mol new dna_base.pdb
mol new 5GZB.pdb


set dnaAll [atomselect 0 all]
$dnaAll moveby [vecinvert [measure center $dnaAll]]

set protAll [atomselect 1 all]
$protAll moveby [vecinvert [measure center $protAll]]

set protProt [atomselect 1 "protein"]

set protDnaAtoms [ atomselect 1 "chain B and resid 4 to 10 and name P"]
puts [$protDnaAtoms get resname]

set dnaAtoms1 [atomselect 0 "chain A and resid 8 to 14 and name P"]
set dnaAtoms2 [atomselect 0 "chain A and resid 16 to 22 and name P"]
puts [$dnaAtoms1 get resname]
puts [$dnaAtoms2 get resname]


set protSe [atomselect 1 "name SE"]
$protSe set name "SD"
$protSe set element "S"
set protMse [atomselect 1 "resname MSE"]
$protMse set resname "MET"

#Begin moving the protein. 

set fm [measure fit $protDnaAtoms $dnaAtoms1]
$protAll move $fm
$protProt set chain A
$protProt writepdb prot_1.pdb

set fm [measure fit $protDnaAtoms $dnaAtoms2]
$protAll move $fm
$protProt set chain B
$protProt writepdb prot_2.pdb
#set dnaAde [atomselect 0 "resname DA"]
#$dnaAde set resname ADE
#set dnaCyt [atomselect 0 "resname DC"]
#$dnaCyt set resname CYT
#set dnaGua [atomselect 0 "resname DG"]
#$dnaGua set resname GUA
#set dnaThy [atomselect 0 "resname DT"]
#$dnaThy set resname THY

set dnaA [atomselect 0 "(chain A and noh) and not (chain A and resid 1 and name P O1P O2P OXT) and not name O2'"]
set dnaB [atomselect 0 "(chain B and noh) and not (chain B and resid 1 and name P O1P O2P OXT) and not name O2'"]
$dnaA set chain C
$dnaB set chain D
$dnaA writepdb dnaC.pdb
$dnaB writepdb dnaD.pdb

exit