Work with protein data bank (pdb) files and awk

Format a pdb with awk for fields: [ATOM] [Atom serial number] [Atom name] [Residue name] [Chain identifier] [Residue sequence number] [x] [y] [z]

Add MODEL # for multiple models pdb files

function mspdb () {
    grep -v 'CRYST1' $1 | awk '{if ($2==1){c+=1;print "MODEL "c}{print $0}}' | sed 's/END/ENDMDL/' > /dev/shm/tmp.pdb && mv -f /dev/shm/tmp.pdb $1
    }

Compute the geometric center from a pdb file

awk '{if ($1 == "ATOM") {sx+=$6;sy+=$7;sz+=$8;n+=1}} END {print sx/n,sy/n,sz/n}' model1.pdb

Just adapt the column numbers for x, y and z depending of the presence of a chain id.

Strip hydrogens from a pdb file

The mktemp -p /dev/shm function ensure that a unique temporary file name is created. This feature is important to run this function in parallel on multiple files.

A word of caution: this function overwrite the input file. Just change the mv $tmpfile $1 to mv $tmpfile newfilename.pdb to avoid this feature.

function stripH () {
    tmpfile=$(mktemp -p /dev/shm)
    awk '{if ($1=="ATOM" && $3 !~ /H/) {c+=1; printf("%-6s%5s %4s %3s %s%4s    %8s%8s%8s\n", $1,c,$3,$4,$5,$6,$7,$8,$9)} \
    else if ($1=="MODEL" || $1=="ENDMDL") {c=0; print $0}}' $1 > $tmpfile && mv $tmpfile $1
}