# find resonance assignment for mutant R19L of Tendamistat using
# lists of peaks automatically identified in the COSY, TOCSY and NOESY spectrum,
# the structures of the wt (and the chemical shifts) of the wt.

parameter suffix rseed
var i

#***************************************************************************#
# parameters specific for a particular protein                              #
#***************************************************************************#

# name for result files
set name     = TS{$suffix}	# name to be used for reports

# data from protein to assign
set dir      = /opt/exp_soft/enmr/BMRZ/garant/2.0/examples/tend	# directory with data
set atomlist = tendmut		# atom list used for writing out assignments
set sequence = tendmutDIANA	# sequence to assign
set cosypl   = COSauto2		# peak lists
set tocsypl  = TOCauto1
set noesypl  = NOEauto2

# comparison with already known assignments
set reftocsy = TendMutTOC_4

# description of related protein
set mutres   = 19		# list of mutated residues

#set freq     = 		# chemical shifts not used
set stdDevHN = 0.15		# standard deviation of shifts for amides
set stdDevAli= 0.05		# standard deviation of shifts for 
				# aliphatic protons

set strucs = $dir/tendwild-
set nrStrucs  = 20
	# minimal allowed distance
set limitdist  = 3
set limitdist2 = 4
	# minimal required number of structures with distance < limitdist
set minStrucs  = 20
set minStrucs2 = 5


#***************************************************************************#
# general parameters and commands                                           #
#***************************************************************************#

set savemacro= writebest	# macro to be used for writing out best
				# assignment
set sizePop  = 100		# number of assignments in population 

spectrum COSY			# use cosy spectrum
   set COSY_acc_w1 = 0.02	# peak pick accuracy in w1
   set COSY_acc_w2 = 0.02	# peak pick accuracy in w2
   load peaks COSY $dir/$cosypl
spectrum NOESY         		# use noesy spectrum
   set NOESY_acc_w1 = 0.02	# peak pick accuracy in w1
   set NOESY_acc_w2 = 0.02	# peak pick accuracy in w2
   load peaks NOESY $dir/$noesypl    # load measured peaks
spectrum TOCSY
   set TOCSY_acc_w1 = 0.02	# peak pick accuracy in w1
   set TOCSY_acc_w2 = 0.02	# peak pick accuracy in w2
   load peaks TOCSY $dir/$tocsypl    # load measured peaks

set pick_acc      = 2.5		# accuracy of peak positions in different
				# spectra is given by:
				#    pick_acc*NOESY_acc_w1, ...

load sequence $dir/$sequence	# sequence to assign
				# sequence for comparison
if ($def('reftocsy')) then
   load comparison sequence  $dir/$sequence
end if

pseudocorrection		# define speudo atom corrections
make coherences			# generate all possible coherences
make couplings			# generate couplings
set i=1				# generate noe's
do
   if ('$mutres(i)' .eq. ' ') break
					# noe's for mutated residues
   make noe ${mutres(i)-1} ${mutres(i)+1}
   eval i = i+1
end do		
do i 1 $nrStrucs			# noe's from the structure
   if ($i.le.9)  then
      set temp = {$strucs}0{$i}.amfm
   else
      set temp = {$strucs}{$i}.amfm
   end if
   load coord $temp
end do
make distance noe floating $minStrucs  $limitdist  1.0
make distance noe floating $minStrucs2 $limitdist2 0.2
make peaks			# generate expected peaks

				# load frequencies from wt
if ($def('freq')) then
   load frequencies $dir/$freq
   define frequency tolerance *  $stdDevAli
   define frequency tolerance HN $stdDevHN
end if

				# load assignments for comparison
if ($def('reftocsy')) then
   load comparison assignments TOCSY $dir/$reftocsy $dir/$atomlist 1.0
end if
				# define report
defaultreport

				# perform optimization
seed random numbers $rseed
opt $sizePop $savemacro

quit