package require topotools
mol new /Users/xadams/CESA/structures/coiled-coil_structures/1weo.pdb
#mol new /Users/xadams/CESA/structures/CESA8pop_alphastalkONLY/namd/merged.psf
mol new merged.psf
mol addfile merged.pdb
set all [atomselect 0 "all"]
set ions [atomselect 0 "ion"]
set arrow [atomselect 0 "alpha and resid 47 to 56"]
set target [atomselect top "alpha and resid 37 to 46 and segname PROA"]
set M [measure fit $arrow $target]
$all move $M
$all set chain A
$ions writepdb ionsA.pdb
set target [atomselect top "alpha and resid 37 to 46 and segname PROB"]
set M [measure fit $arrow $target]
$all move $M
$all set chain B
$ions writepdb ionsB.pdb
set target [atomselect top "alpha and resid 37 to 46 and segname PROC"]
set M [measure fit $arrow $target]
$all move $M
$all set chain C
$ions writepdb ionsC.pdb

set midlist {}
set mol [mol new "ionsA.pdb"]
lappend midlist $mol
set mol [mol new "ionsB.pdb"]
lappend midlist $mol
set mol [mol new "ionsC.pdb"]
lappend midlist $mol
set mol [::TopoTools::mergemols $midlist]
animate write pdb mergedions.pdb $mol