!<beginning of match1ds.edp>
!! copyright by X. Cai Zhang (000602)

! This macro does a simple sequence alignment 
!   and sets the OCC field to the alignment score 
!   (i.e. [-1.5,1.5] & -1.6 for deletion).
! useful for displaying sequence homology.

! Syntax:
! @match1ds target_sequence chain_mark
! example: to align chain a to the target_sequence (t.seq), type 
! @match1ds t.seq a

reset
write pseudo_.pdb 'REMARK This pseudo pdb file is created by match1ds.edp.'
seq2pdb $(p1) '(100a1)'
close
read pseudo_.pdb t

! sequence homology search
{ca | chain t ; group tmpa }
initialize
setenv -s verbose 2
{ ca | chain $(p2) ; setw -1.6 | match1d tmpa suba -1.6 1.0 0.5 0.1 30}
setenv verbose 0

pause
initialize
{ ca | chain $(p2) ; group tmpa ; group tmpb}

mkfile tmp_m1_.edp eof
loop:
initialize
para occ tmpa w  exit
para id  tmpb id exit
zone $(id) ; more ; setw $(occ)
goto loop
eof

setenv -s maxerr 1024 exit
setenv -s echo 0
@tmp_m1_
setenv -r maxerr
setenv -r echo 
initialize
chain $(p2)

!<end of match1ds.edp>