Thomas,thanks for help- I'll try to test your script!
Jed, many thanks too!
if I understood correctly align.profit should contain thefollowing lines:
# using ProFIT to align the model to 2hi4
open $PROFIT, "> align.profit" or die "Cannot open file align.profit\n";
print $PROFIT "ATOMS CA\n";
print $PROFIT "ZONE 34-513:1-480\n";
print $PROFIT "FIT\n";
print $PROFIT "WRITE $folder/$dir/$pdbnew\n";
close $PROFIT;
shouldn't it?
that that file is provided to 1 command line
`profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
$folder/$dir/$pdbnew`;
where 2hi4.pdb is my ref
$pdbnew variable assosiated with the target pdb
one question about align.profit: will the output aligned mobile.pdb consist
of all atoms? I've found that only CA atoms are used for the superimposition
print $PROFIT "ATOMS CA\n";
James
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