Objective

Here you will learn how to build crystallographic symmetry for a PDB structure.

Background

Most structure files contain some information regarding symmetry such as (i) crystallographic group eg. P2121 that determine N (depends on a group) transformations for the atoms in the asymetric unit and (ii) 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 ICM to generate symmetry related parts of the density or molecular objects.

Instructions

1. To generate symmetry related molecules we first need to read a PDB file into ICM (for an example choose 1crn)
2. Display the structure and select some residues around which you wish to generate the symmetry related molecules.
3. Tools/Xray/Crystallograhic Cell.
4. Select the radius around your selction from which you wish to construct the symmetry related molecules.
5. Tick the create symmetry related molecules box.
6. Select whether you want the symmentry generated molecules to be merged into the original PDB object.
7. Select whether you wish for the symmetry related generated molecules to be displayed. 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:
8. Select the Display tab hold down on the wire button and select the color by chain option.

Manual References (Web Links)

Symmetry