! <beginning of match3d.edp>
!! copyright by X. Cai Zhang (modified on 010607)

! This macro calculate the matrix from one protein molecule to another.
! It require v01b or higher version EDPDB to run this macro. 
! A PDB file, tmp_.pdb, is written to output the rotated-translated molecule.
! Note: the PDB file should not contain a 'j' chain.
! also see: matchzn.edp, match1ds.edp, match1d.edp

! Syntax: 
! @match3d target_chain moving_chain

! example: to overlay chain b to chain a, type 
! @match3d a b

! define secondary structures
initialize ; ca ; setw 0.0
@find_helices
setw 1.0
@find_strands
setw 2.0

! define molecule A and B
parameter ch_a = $(p1)
parameter ch_b = $(p2)

! overlay B to A based on secondary structure alignment
initialize ; ca | chain $(ch_a)  ; group a 
initialize ; ca | chain $(ch_b)  ; group b

setenv -s verbose 2
match3d a 4 5.0 rtn_.txt 
!!            ^    parameters that can be varied
if (-i status == -3 ) goto abort

chain $(ch_b) ; rtn file rtn_.txt ; initialize

ca ; seti ; setw 1.0 ; initialize

! refine the overlay based on 
!  maximizing the number of matched atoms 
!  and minimizing the overall coordinate difference

setenv verbose 0
@align3d $(ch_a) $(ch_b) 7.0
!!                        ^    a parameter that can be varied
if ( -i istatus == -1 ) goto abort
@align3d , , 6 
if ( -i istatus == -1 ) goto abort
@align3d , , 5
if ( -i istatus == -1 ) goto abort
@align3d , , 4
if ( -i istatus == -1 ) goto abort
@align3d , , 3     
if ( -i istatus == -1 ) goto abort
@align3d , ,     
if ( -i istatus == -1 ) goto abort

system rm tmp_.pdb ; write tmp_.pdb ; close; reset 

read tmp_.pdb j ; chain j ; group jnk ; initialize 

chain $(ch_b) ; overlay jnk $(ch_b)2$(ch_a)_.txt ; initialize
setenv -r verbose

! NOTE THAT THE ORINGINAL FILE(S) HAVE NOT BEEN CHANGED YET.
!
! match3d mainly does two things. first it calculates 
!  the rotation-translation matrix from one molecule ($(ch_b))
!  to the other ($(ch_a)), named as $(ch_b)2$(ch_a)_.txt; second, it creates a PDB file, 
!  tmp_.pdb of the rotated-translated molecule ($(ch_b)). 
!  the input PDB file(s) are reset to the oringinal ones
!  at the end of the procedure.
! Suggested action:
!  initialize ; chain $(ch_b) ; rtn file $(ch_b)2$(ch_a)_.txt
!<end of match3d.edp>
return

abort: ; setenv -r verbose
!<abort: match3d.edp>