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Split NMR-style multiple model pdb files into individual models: Difference between revisions
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Split NMR-style multiple model pdb files into individual models (edit)
Revision as of 21:14, 3 June 2016
, 3 June 2016no 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. | ||
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/awk one-liner == | ||
bash -sf | |||
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 models.pdb > model_%03d.pdb\n", $1-1,NR/2;}' | bash -sf | |||
== Bash script == | |||
i=1 | |||
while read -a line; do | |||
echo "${line[@]}" >> model_${i}.pdb | |||
[[ ${line[0]} == ENDMDL ]] && ((i++)) | |||
done < /path/to/file.pdb | |||
== Awk script == | |||
Should be called as | |||
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 == | |||
$base='1g9e';open(IN,"<$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"} | |||
} | |||
== Python script == | |||
For this kludgy version using Python 2.x, you need to paste the entire PDB file into the script where it says "PASTE YOUR PDB FILE TEXT HERE". | |||
You can fork [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py the code here at Github]. | |||
(A more full-featured version there that you can just point at your file [,or a folder of files,] using an argument on the command line can be found [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py here at Github]. ) | |||
PDB_text = """ | |||
PASTE YOUR PDB FILE TEXT HERE | |||
""" | |||
model_number = 1 | |||
new_file_text = "" | |||
for line in filter(None, PDB_text.splitlines()): | |||
line = line.strip () #for better control of ends of lines | |||
if line == "ENDMDL": | |||
# save file with file number in name | |||
output_file = open("model_" + str(model_number) + ".pdb", "w") | |||
output_file.write(new_file_text.rstrip('\r\n')) #rstrip to remove trailing newline | |||
output_file.close() | |||
# reset everything for next model | |||
model_number += 1 | |||
new_file_text = "" | |||
elif not line.startswith("MODEL"): | |||
new_file_text += line + '\n' | |||
Back to [[Useful scripts (aka smart piece of code)]] | |||