Dear All,

I am trying to write an script to calculate geometric centre of selected residues of a protein structure. Say I have a PDB file (a text containing the x, y, and z coordinates of atoms of a protein). I want to extract the X coordinates of the atoms belonging to the interested residues and get the Max and Min values for X coordinates and then calculate the X coordinate for the geometric centre as followings: X(cent) = (X(max) - X(min))/2. The same will go for Y(cent) and Z(cent). To do this it is better to have something to read in the X coordinates for the interested atoms from the X coordinate column in the PDB file and find the X(max) and X(min). The way that I do this is to read these values and put them in a file (say temp.dat). Then I sort the file ascending and descending based on different columns (i.e., x, y, and z colunms) and extract the max and min for X, Y and Z as you can see below:

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#/bin/csh
echo -n "name of file (full path; incl. extension):"
set INFILE = $<
echo -n "name of output file (full path):"
set OUTFILE = $<
echo -n "Specify the starting residue number:"
set START = $<
echo -n "Specify the last residue number:"
set END = $<
@ END ++
@ START --
#
#
#
#
awk ' ($1 == "ATOM" && ( $5 > '$START' ) && ( $5 < '$END' )){{printf("%10.3f%10.3f%10.3f\n", $6, $7, $8)}};' $INFILE >>! $OUTFILE
#
sort $OUTFILE | set Xmin = `head -1 | awk '{printf("%10.3f\n", $1)};'`

sort -n +1 $OUTFILE | set Ymin = `head -1 | awk '{printf("%10.3f\n", $2)};'`

sort -n +2 $OUTFILE | set Zmin = `head -1 | awk '{printf("%10.3f\n", $3)};'`

sort -r $OUTFILE | set Xmax = `head -1 | awk '{printf("%10.3f\n", $1)};'`

sort -rn +1 $OUTFILE | set Ymax = `head -1 | awk '{printf("%10.3f\n", $2)};'`

sort -rn +2 $OUTFILE | set Zmax = `head -1 | awk '{printf("%10.3f\n", $3)};'`

echo $Xmin $Xmax $Ymin $Ymax $Zmin $Zmax
exit 1
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The problem is that I can't use the Xmin, Xmax, Ymin, ... to calculate X(cent), Y(cent), and Z(cent), using "expr" command. E.g., for the following command, I get the following error:

>expr $Xmin - $Xmin

non-numeric argument

I guess there is something wrong with these variables and they are character strings and not numbers. I will appreciate it if you give me some input.

Cheers, Siavoush