ITAS - Rapid Determination of Protein Structures in Solution Using NMR Dipolar Couplings

# Remove the unnecessary files

com = "rm -f cs_source.tab cs_source_p.tab cs_source_f.tab cs_source_d.tab"

system(com)

# Before restarting check Result directory

# If final result directory is ok, then fix the prevAss.

# If final result directory is not ok, then remove the result directory and fix the prevAss.

# Check reference pdb file.

########################## INPUT PARAMETERS #################################

set com_name gwdu

########################### Define Paths of programs ##############

set pfold /home/mpg1/MBPC/yjung/progs/blast/rosettaNMR-v1_2/rosetta_source/pFOLD.New.lnx

global Rundir pfold make_frag mars molmol bindir ext1 ext2 dctab cstab\

protein_name chain_id iter abext1 abext2 firstAA lastAA firstDC lastDC\

PALES prevAss step_2 step_3 com_num com_name marsHome iter_num time_run

# ---> Step_0 Run MARS without structure... <---set Rundir [exec pwd]

catch {exec cp $bindir/paths.txt $Rundir/.}

set fastaName [exec awk {{if($1=="sequence:") print $2}} mars.inp]

set dctab [exec awk {{if($1=="dcTab:") print $2}} mars.inp ] set cstab [exec awk {{if($1=="csTab:") print $2}} mars.inp ]

if {![file isfile $protein_name$chain_id.fasta]} { exec cp $fastaName $protein_name$chain_id.fasta }

if {![file isdirectory Result0]} { puts "Changing directory to $Rundir"

puts "Current path: [exec pwd]"

puts "Protein name: $protein_name"

puts "DC table: $dctab"

puts "CS table: $cstab"

puts "Iteration number: $iter"

set call [construct_mars_input 0 "NO"]

# set mars_input mars.inp

puts "Running mars without a structure"

catch {exec $mars mars_temp.inp >& mars.log } result catch {exec mkdir Result0} result

catch {eval exec cp [glob ana*] Result0} result catch {eval exec cp [glob assignment*] Result0} result puts "Total assginalbe number:\

[exec awk {{for(i=3;i<=NF;i++) if($i!=-9999){num++;break}}END{print num}} Cs_expt.tab]\

([exec awk {{if($3!=-9999 && $4!=-9999) num++}END{print num}} Cs_expt.tab])"

puts "MARS assigned successfully without structure\n\n\n"

B.4 ITAS 157

set iniDir 1 } else {

for {set iniDir 1} {$iniDir <= $iter} {incr iniDir} { if {![file isdirectory Result$iniDir]} {

break }

} }

exec awk -f $marsHome/making_expt_dc.awk $dctab

set BestAssignName "ana_bestfirst_assignment.txt"

set ReliableAssignName "ana_reliable_assignment.txt"

########################### For number of Iterations######################

for {set i $iniDir} {$i <= $iter} {incr i} {

# ---> Step_1 Preparing Rosetta input...

<---# Make a directory and chagne Result directory catch {exec mkdir Result$i }

set Resdir Result$i

# Make Rosetta input

catch {exec awk -f $bindir/RemoveAmbiguous.awk\

argv=$ReliableAssignName $ReliableAssignName > mars.ara } result catch {exec awk {{print $2 , $1 }} mars.ara > mars.cpk } result catch {exec sort -k1n mars.cpk > mars.spk } result

catch {exec awk -f $bindir/RemoveAmbiguous.awk argv=mars.spk mars.spk > mars.inv } result catch {exec awk {{print $2 , $1 }} mars.inv > mars.ass } result

catch {exec $bindir/rosetta_format.com } result

# Check Reliable assignment

set thisAss [exec awk {{if(NF==2) count++}END{print count}} mars.ass]

puts "Result$i"

puts "Previous assignment number: $prevAss"

puts "The TOTAL assignment number of reliable assignments: $thisAss"

# puts "[exec awk {{if($1==$2 && $2!=1) print}} mars.ass]"

if { $thisAss > $prevAss } {

puts "RELIABLE ASSIGNMENTS are taken for the Rosetta input."

} \ else {

if {[file exists $BestAssignName ]} {

catch {exec $bindir/mostprobass $BestAssignName mars.mpa } result catch {exec awk {{print $2 , $1 }} mars.mpa > mars.cpk } result

catch {exec sort -k1n mars.cpk > mars.spk } result catch {exec awk -f $bindir/RemoveAmbiguous.awk\

argv=mars.spk mars.spk > mars.inv } result catch {exec awk {{print $2 , $1 }} mars.inv > mars.ass } result catch {exec $bindir/rosetta_format.com } result

# Check Bestfirst assignment

puts "BEST-FIRST ASSIGNMENTS are taken for the Rosetta input"

puts "The TOTAL assignment number of most probable best-first assignment:\

[exec awk {{if(NF==2) count++}END{print count}} mars.ass]"

} }

# Check Rosetta CS input

catch {exec awk -f $bindir/csRosetta.awk Cs_expt.tab > inputAll_CS.tab } result

puts "The TOTAL number of pseudo-residues used for Rosetta: \ [exec awk {BEGIN{de=9999}{for(i=3;i<=NF;i++) if($i!=de){num++;break}}\

END{print num}} assignedCsRosetta.tab]\

([exec awk {{if($7!=9999) num++}END{print num}} assignedCsRosetta.tab])"

# Check Rosetta RDC input set count [exec awk {

BEGIN{

set count [exec awk {BEGIN{de=9999;count=0} $3~/^N$/ && $5~/^C$/ {if($7!=de) count++}\