Split NMR-style multiple model pdb files into individual models

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Revision as of 16:43, 15 December 2010 by Pozharski (talk | contribs)
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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 named 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

Bash script


while read -a line; do

echo "${line[@]}" >> model_${i}.pdb

[[ ${line[0]} == ENDMDL ]] && ((i++))

done < /path/to/file.pdb

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"}


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