Theory

Molecular objects and 3D density maps may contain information about crystallographic symmetry. It consists of the following parameters:

1. Crystallographic group eg. P2121 that determine N (depends on a group) transformations for the atoms in the asymetric unit.
2. Crystallographic cell parameters A, B, C, Alpha, Beta and Gamma

To generate the coordinates within one cell one needs to apply N transformations and then to generate neigboring cells the content of one cell needs to be translated in space according to the cell position.

ICM has a function which generates crystallographic neighbors for the selected atoms. For large proteins it is impractical to generate neighbors for the whole molecule due to the high number of atoms in all neighboring molecules.

This information allows to generate symmetry related parts of the density or molecular objects.

To generate symmetry related molecules around a selection of atoms:

• Read a PDB file into ICM. For instruction see the section entitled Finding a PDB Structure.
• Display the structure and select the residues around which the symmetry will be generated. For information on how to select residues see the Making Graphical Selections section.

• Select the menu Tools/Xray/Crystallograhic Cell.

A data entry box as shown below will be displayed.

• Select the radius around your selction from which you wish to construct the symmetry related molecules.
• Tick the create symmetry related molecules box.
• Select whether you want the symmentry generated molecules to be merged into the original PDB object.
• Select whether you wish for the symmetry related generated molecules to be displayed.
• Click OK.

The crystallographic symmetry neighbors will be displayed in the Workspace Panel along with the crystallographic cell.

For packing analysis and display you can color each symmetry unit a different color as described in the Structural Representations Color section. This is shown in the picture below.