May 17 2013
Molecular objects and 3D density maps may contain information about crystallographic symmetry. It consists of the following parameters:
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:
A data entry box as shown below will be displayed.
The crystallographic symmetry neighbors will be displayed in the Workspace. By default the object will have the object name + "Sym" and each of the neighbors will be individual molecules.
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.
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