[PyMOL] Generate Symmetry mates

PyMOL can show crystal packing information by generating the “symmetry mate”. Once a crystal structure is loaded, go to “A”, select “generate”, then “symmetry mates”. There are options to display +/- one unit cell and within xx angstrom. Depending on the crystal size, the symmetry expansion can be very different.

Below is an example using a 76-aa protein called ubiquitin (RCSB PDB ID: 1UQB). This crystal space group is P212121 and once the symmetry is expanded, the P212121 3-screw dimension is clearly displayed.

Once 1UBQ is loaded, PyMOL 2.3 automatically display structure in cartoon mode, water molecules are also shown. Then go to action, select generate and choose symmetry mates like what is shown in the PyMol screen shot.

Below are symmetric units of 1UBQ in PyMOL. The yellow boxed objects are individual unit cells generated based on P212121 symmetry. The original object is colored in red and full view (zoomed out) of 1UBQ with 6Å symmetry mates are shown in the end.