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Jump to navigationJump to searchSplit NMR-style multiple model pdb files into individual models (edit)
Revision as of 15:08, 16 December 2010
, 15:08, 16 December 2010no edit summary
This one-liner splits the file models.pdb into individual pdb files named model_###.pdb.
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", $1-1,NR/2;}' | bash -sf
== Bash script ==
== Bash script ==
i=1
while read -a line; do
echo "${line[@]}" >> model_${i}.pdb
[[ ${line[0]} == ENDMDL ]] && ((i++))
done < /path/to/file.pdb
Should be called as
Should be called as
awk -f script.awk < models.pdb
awk -f script.awk < models.pdb
BEGIN {file = 0; filename = "model_" file ".pdb"}
/ENDMDL/ {getline; file ++; filename = "model_" file ".pdb"}
{print $0 > filename}
== Perl script ==
== 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"}
}
Back to [[Useful scripts (aka smart piece of code)]]
Back to [[Useful scripts (aka smart piece of code)]]
