Split NMR-style multiple model pdb files into individual models: Difference between revisions
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This one-liner splits the file models.pdb into individual pdb files names model_###.pdb. | This one-liner splits the file models.pdb into individual pdb files names model_###.pdb. | ||
grep -n 'MODEL\|ENDMDL' models.pdb | | '''grep -n 'MODEL\|ENDMDL' models.pdb | ''' | ||
cut -d: -f 1 | | '''cut -d: -f 1 | ''' | ||
awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp > model_%03d.pdb\n", $1-1,NR/2;}' | | '''awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp > model_%03d.pdb\n", $1-1,NR/2;}' | ''' | ||
bash -sf | '''bash -sf''' | ||
== Perl script == | == Perl script == | ||
$base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0; | '''$base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0;''' | ||
foreach $line(@indata) { | '''foreach $line(@indata) {''' | ||
if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next} | '''if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next}''' | ||
if($line =~ /^ENDMDL/) {next} | '''if($line =~ /^ENDMDL/) {next}''' | ||
if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"} | '''if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"}''' | ||
} | '''}''' | ||
Back to [[Useful scripts (aka smart piece of code)]] | Back to [[Useful scripts (aka smart piece of code)]] |
Revision as of 16:51, 14 December 2010
This assumes that you have a correctly formatted pdb file that contains both MODEL and ENDMDL records.
Bash/awk one-liner
This one-liner splits the file models.pdb into individual pdb files names model_###.pdb.
grep -n 'MODEL\|ENDMDL' models.pdb | cut -d: -f 1 | awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp > model_%03d.pdb\n", $1-1,NR/2;}' | bash -sf
Perl script
$base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0;
foreach $line(@indata) {
if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next}
if($line =~ /^ENDMDL/) {next}
if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"}
}