replace - Column replacement with awk, with retaining the format

Question

This is file a.pdb:

ATOM      1  N   ARG     1       0.000   0.000   0.000  1.00  0.00           N
ATOM      2  H1  ARG     1       0.000   0.000   0.000  1.00  0.00           H
ATOM      3  H2  ARG     1       0.000   0.000   0.000  1.00  0.00           H
ATOM      4  H3  ARG     1       0.000   0.000   0.000  1.00  0.00           H

And this is file a.xyz:

16.388 -5.760 -23.332
17.226 -5.608 -23.768
15.760 -5.238 -23.831
17.921 -5.926 -26.697

I want to replace 6,7 and 8th column of a.pdb with a.xyz columns. Once replaced, I need to maintain tabs/space/columns of a.pdb.

I have tried:

awk 'NR==FNR {fld1[NR]=$1; fld2[NR]=$2; fld3[NR]=$3; next} {$6=fld1[FNR]; $7=fld2[FNR]; $8=fld3[FNR]}1' a.xyz a.pdb 

But it doesn't keep the format.

Answer 1

This is exactly what the 4th arg for split() in GNU awk was invented to facilitate:

gawk '
NR==FNR { pdb[NR]=$0; next }
{
    split(pdb[FNR],flds,FS,seps)
    flds[6]=$1
    flds[7]=$2
    flds[8]=$3
    for (i=1;i in flds;i++)
        printf "%s%s", flds[i], seps[i]
    print ""
}
' a.pdb a.xyz

ATOM      1  N   ARG     1       16.388   -5.760   -23.332  1.00  0.00           N
ATOM      2  H1  ARG     1       17.226   -5.608   -23.768  1.00  0.00           H
ATOM      3  H2  ARG     1       15.760   -5.238   -23.831  1.00  0.00           H
ATOM      4  H3  ARG     1       17.921   -5.926   -26.697  1.00  0.00           H