How to extract specific frames/model from a multi model pdb file?

Question

I have a multi model pdb file and would like to extract the last frame or any other frame from it.

Answer 1

Do you have access to OpenBabel to run from the terminal?

For the purpose of demonstration, the example following is demonstrated on a file listing SMILES strings. However, the concept may be applied on a .pdb with multiple models (and equally works well enough on multi-model .sdf).

The input file input.smi is a small set of aromatics. SMILES strings and labels are tabulator separated:

c1ccccc1    Compound 1
c1(cc(cc(c1)C)C)C   Compound 2
c1(ccc(cc1)C)C  Compound 3
c1(ccccc1)C Compound 4
n1ccccc1    Compound 5
n1cnccc1    Compound 6
n1cncnc1    Compound 7

My interest is on the p-xylene only (i.e., Compound 3). With the instruction

obabel -ismi input.smi -f 3 -l 3 -osmi -O interest.smi

OpenBabel anticipates the input file to contain SMILES (-ismi), starts processing with the third model entry onward (-f 3, line/model counting index in the file starts by 1), accessing all entries up and including the third one (-l 3) in this file. The output, to contain SMILES and their labels (if present) is formatted (-osmi) and written permanently (-O) into file interest.smi which eventually contains

 c1(ccc(cc1)C)C  Compound 3

Since OpenBabel run from CLI is agnostic about file extensions, your processing of .pdb to be read, and to be written requires an adjustment of the input/output parameters e.g., in the pattern of

obabel -ipdb input.pdb -f 3 -l 3 -opdb -O interest.pdb

---

This approach equally allows to extract a contiguous set of entries, e.g.

obabel -ismi input.smi -f3 -l5 -osmi -O interest.smi

to process 3 molecules at once. The toggles -f and -l may be used independently of each other, and spaces between them and their then mandatory integer parameters may be omitted. The approach however is unable to pick a set molecules in the mixed pattern like (1, 3-5, 7).

Said selection may be achieve from obgui, too:

Answer 2

file=test.pdb #pdb file 
frame=10 # frame number to extract 
x_frame=$(egrep "MODEL.* $frame$" $file)
sed -n "/$x_frame/,/ENDMDL/p" $file > ${file::-4}_frame_$frame.pdb

output file will be written as filename_frame_10.pdb

---

The bash script below provides easier (repeated) access to the functionality described:

#!/bin/bash

# Extract a specific .pdb from a multi model .pdb file

# Save this bash script as pick_pdb.sh and run
#
# bash pick_pdb.sh test.pdb 3
#
# to write test_frame_3.pdb as new file.  Relies on bash and sed.

if [[ -z "$1" ]] ; then
    printf "Check how to use this bash script with
        bash pick_pdb.sh -h  \n"

elif [[ "$1" == "-h" || "$1" == "--help" ]] ; then
    printf "Export a specific model from multi model .pdb file.

E.g., to extract the third model from intput.pdb,

    bash pick_pdb.sh input.pdb 3

writes file input_frame_2.pdb.  \n"


else
    file="$1"
frame="$2"

    filebase="$(basename "$file" .pdb)"
    output=${filebase}_frame_$frame.pdb

    x_frame=$(egrep "MODEL.* $frame$" "$file")
    sed -n "/$x_frame/,/ENDMDL/p" "$file" > "$output"
fi

Answer 3

You can use the Python script multiple_model_PDB_file_splitter:

# multiple_model_PDB_file_splitter.py by Wayne Decatur
# ver 0.2
#
#*******************************************************************************
## PURPOSE: Takes a formatted pdb file with multiple models and splits each model
# into individual files. Requires the PDB file include both MODEL and ENDMDL


# records for each of the models.

# Originally developed in Python 2.7, but confirmed to work in Python 3.6.
#

You can download it from here.

Other useful script from the same author can be download here.