c2x and Visualising Symmetry with Jmol

(Those producing CIF files from versions of c2x <=2.40b will need to ensure that the first symmetry operation in the CIF file is listed as "x,y,z", not "+x,+y,+z", else Jmol becomes confused.)

Continuing from the symmetry overview page, we can launch Jmol, and, with File | Open calcite.cif.

Jmol with asymmetric calcite cell

But this unhelpfully shows just the symmetry-inequivalent atoms. To see the symmetrised set, find the Jmol console window (File | Console) and type

$  load "calcite.cif" {1,1,1}

Jmol with full calcite cell

If one wishes to tile the unit cell, it should be done at this point by specifying more repeat units in the parentheses, e.g. {2,2,1} for two units in the a and b directions.

The console window is also needed for listing and showing the symmetry operations.

$ show symmetry
Symmetry Information:
model #1.1; name=c2x
Spacegroup: -P 3* 2n [R -3 c:r] #167
Number of symmetry operations: 12
Symmetry Operations:
$ show symop 10
n-glide plane|translation: 1/2 1/2 1/2
$ draw symop 10
z+1/2,y+1/2,x+1/2 n-glide plane|translation: 1/2 1/2 1/2

Jmol with calcite and glide plane

The glide plane is shown, and the translation vector is also shown in yellow.

$ draw symop 11
-y+1/2,-x+1/2,-z+1/2 C2 axis

Jmol with calcite and C2 axis

The axis is shown together with a curved arrow showing the rotation, not visible in this example.

To show multiple elements at once, it is necessary to give them explicit, distinct, object IDs.

$ draw a1 symop 7
-x+1/2,-z+1/2,-y+1/2 C2 axis
$ draw a2 symop 9
-z+1/2,-y+1/2,-x+1/2 C2 axis
$ draw a3 symop 11
-y+1/2,-x+1/2,-z+1/2 C2 axis

Jmol with calcite and C2 axes

To delete one of these elements, use

$ draw a2_* delete

The underscore and asterix after the ID are necessary as the element is drawn using multiple objects prefixed with the ID specified.