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Split NMR-style multiple model pdb files into individual models: Difference between revisions
Split NMR-style multiple model pdb files into individual models (edit)
Revision as of 16:42, 14 December 2010
, 14 December 2010no edit summary
(Created page with 'This assumes that you have a correctly formatted pdb file that contains both MODEL and ENDMDL records. It gets split into individual pdb files names model_###.pdb. grep -n 'MOD…') |
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This assumes that you have a correctly formatted pdb file that contains both MODEL and ENDMDL records. | 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 | | grep -n 'MODEL\|ENDMDL' models.pdb | | ||
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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 == | |||
$base='1g9e';open(IN,"<$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"} | |||
} | |||