Split NMR-style multiple model pdb files into individual models

From CCP4 wiki

This assumes that you have a correctly formatted pdb file that contains both MODEL and ENDMDL records.


Bash/awk one-liner[edit]

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[edit]

 i=1
 while read -a line; do
   echo "${line[@]}" >> model_${i}.pdb
   [[ ${line[0]} == ENDMDL ]] && ((i++))
 done < /path/to/file.pdb


Awk script[edit]

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[edit]

 $base='1g9e';open(IN,"<$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[edit]

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 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 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'


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