coordinate <coordinate-statement> end


<coordinate-statement> :==

{<coordinate-read-statement>}
swap [selection=<atom-selection>]
   Exchanges main and comparison coordinate sets:
   x,y,z <--> xcomp,ycomp,zcomp; b and q remain unaffected.

copy [selection=<atom-selection>]
   Copies main set into comparison coordinate set:
   xcomp:=x, ycomp:=y, zcomp:=z; b and q remain unaffected.

init [selection=<atom-selection>]
   Initializes main set: x:=9999.0, y:=9999.0, z:=9999.0

rotate [center=<vector>] [selection=<atom-selection>] <matrix>
   Rotates selected atoms in x,y,z coordinate set by <matrix>
   about the defined rotation center. Default center is (0,0,0).

symmetry <symmetry-operator> [selection=<atom-selection>]
   Apply symmetry operation to main set. <symmetry-operator> is
   from the international tables, e.g. (-x,y+1/2,-z), and must include
   parenthesis. The operator is applied in fractional space. The unit
   cell constants must be defined.

translate [selection=<atom-selection>] vector=<vector> [distance=<real>]
   Translate the main set by vector <vector> or if a distance is
   also specified by this distance along the vector <vector>.

orient [mass=<logical>] [lsq=<logical>] [sele=<atom-selection>]
   Transforms coordinates into principal axis system.

fit [mass=<logical>] [lsq=<logical>] [sele=<atom-selection>]
   Calculate and apply least squares fit to comparsion coordinate set.

rms [mass=<logical>] [sele <atom-selection>]
   Show RMS difference between main and comparison coordinate sets.

orthogonalize [selection=<atom-selection>]
   Orthogonalize main set using unit cell dimensions defined in xray.

fractionalize [selection=<atom-selection>]
   Fractionalize main set using unit cell dimensions defined in xray.

rgyration [mass=<logical>] [factor=<real>] [sele=<atom-selection>]
   Calculate radius of gyration for selected atoms.

<coordinate-read-statement> :==

disposition=main|comp|reference|derivative
   Destination for read coordinates.

selection=<atom-selection>
atom <pdb-atom-record>
   Brookhaven Protein Databank atomic coordinate record.

remark <string>
   Brookhaven Protein Databank remark statement.

<pdb-atom-record> :==

<integer> <atom> <resname> <resid>
          <real> <real> <real> <real> <real> <segid>

   The following format is expected:

1        10        20        30        40        50        60        70
|        |         |         |         |         |         |         |  
ATOM   1223  O   GLY   153     -11.704  -9.200    .489  1.00  0.80      MOL1
      ccccc ''''Iyyy O,,,,L   ........>>>>>>>>////////ppppppiiiiii iii  iiii
      ^ atom number   ^ resid ^ x     ^ y     ^ z     ^ q   ^ b         ^ segid
            ^ atom name   ^ insertion character
            ^ additional character for some atom names (mostly hydrogens)
                 ^ residue name
                     ^ chain identifier