Align molecule

(http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/)
mol delete all

mol load psf pope.psf pdb pope_move.pdb
global popemol
set popemol [molinfo top]
mol load psf protein.psf pdb protein.pdb

display projection orthographic

mol modselect 0 $popemol "name P"
mol modstyle 0 $popemol VDW

puts {
     1. Switch to Move Molecule mode by moving the mouse into the graphics
        window and pressing the 8 key.  The cursor should now have the form
        of a cross-hair.

     2. While holding down the shift key, click on one of the protein atoms
        and drag the mouse.  You should see just the protein rotating
        around the atom you picked.  Try to align the axis of the protein
        with an imaginary line coming out of the screen, so that it's
        perpendicular to the membrane.  If you accidentally rotate the
        whole scene instead of just the protein, type "display resetview"
        in the text console to get back to the original view.

     3. Type "rotate x by -90" in the text console.  Now you want to center
        the protein between the phosphate atoms of the bilayer.  This time,
        click and hold on one of the protein atoms _without_ holding down
        shift.  Move the protein up and down until it's centered.

     4. Switch back to the orginal view with "display resetview".  If the
        protein looks good, you can go on to the next step; otherwise repeat
        steps 2 and 3 above.
}