Sep 4 2023
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.
The crystal structure of a protein is often discussed in terms of its unit cell. The unit cell is a box containing one or more motifs, a spatial arrangement of atoms. The units cells are tiled in three-dimensional space to describe the crystal. The unit cell is given by its lattice parameters, the length of the cell edges and the angles between them, while the positions of the atoms inside the unit cell are described by the set of atomic positions measured from a lattice point.
To display the crystal cell of a PDB structure:
The crystallographic cell will be displayed as a box as shown below.
It is very useful to know how a protein from the PDB may look in a biological environment. The PDB entries solved by X-ray crystallography and deposited in the PDB contain the information about the crystal structure rather than the biologically relevant structure. For example, for a viral capsid only one instance of capsid protein complex will be deposited and only one or two molecules of haemoglobin that is a tetramer in solution maybe deposited.
In some other cases the asymmetric unit may contain more than one copy of a biologically monomeric protein. ICM reads the biological unit information and has a tool to generate a biological unit. Not every PDB entry has the biological unit information.
A gallery of images created using the ICM Biomolecule generator is shown below:
Left: PDB: 1DWN Bacteriophage Pp7 From Pseudomonas Aeruginosa At 3.7 A Resolution Right: PDB: 1C8E Feline Panleukopenia Virus Empty Capsid Structure At 3.0 A Resolution
Left: PDB: 1AL2 P1/Mahoney Poliovirus, Single Site Mutant V1160I At 2.9 A Resolution Right: PDB: 1LP3 Adeno-Associated Virus (Aav-2), A Vector For Human Gene Therapy At 3.0 A Resolution
To generate a biological unit with ICM:
An electron density map is a representation of a crystal structure based on the diffraction data. The map is constructed by a summation of waves of known phase, amplitude and frequency using Fourier transform. The electron density map of a protein can be viewed along with the pdb structure. The easiest way to view the electron density map is to contour and convert it into a graphical object (mesh).
A figure showing the electron density contours surrounding the ATP molecule in pdb entry 1ATP.
To load an electron density map:
The map will be represented in the ICM Workspace as shown below.
The map can be displayed as shown below however a clearer way of representing the density is to contour the map into a graphical object (mesh) as described in the following section.
To display the original crystallographic cell of an electron density map:
To contour an electron density map and display as a graphical object:
The sigma level can be changed interactively in the ICM workspace as shown below.
For some applications, such as trying to fit a structure to a density map, you may want to extract a sub map and convert to a grid. You can do this by
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