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Assuming no empty field/line in the input, try:
awk -F\; '{for(i=1;i<=NF;i++) count[$i,i]++;if(max<NF) max=NF}
END{for(i=65;i<=90;i++) {
c=sprintf("%c",i);
printf("%s",c);
for(j=1;j<=max;j++)
...

Try this:

awk -F " ; " '{
t[$1]
x[$1,$2] = $NF
} END {
for(h in t) printf ";%s", h;
printf "\n"
for(v in t) {
printf "%s", v
for(h in t)
if((h...

Use >>OUT instead of >OUT.

If your system really does support enough arguments:

# Set $1, $2, ... to the list of files you want.
set -- snap[0-9][0-9][0-9][0-9].pdb.OW.msd

# Loop while there's more than 1 file in the...

I don't think your code blocks are doing what you think they do. Some of them look pointless (a code block that does only $4=="TCO" ? You probably meant to use () instead of {}, and put it...

Hi grincz,

One way using awk:

$ cat infile
ATOM 4688 HG1 PRO A 322 18.080 59.680 137.020 1.00 0.00
ATOM 4689 HG2 PRO A 322 18.850 61.220 137.010 1.00 0.00 ...