CrystalMaker Guide: Brookhaven PDB Files

A data format used by the Brookhaven Protein Data Bank (PDB).

The Brookhaven Protein DataBank contains a wealth of information on macromolecules. The files list orthogonal coordinates for individual molecules. The example below corresponds to glycine:-

ATOM 1 N GLY 1 0.162 -0.202 0.000 1.00 0.00 ATOM 2 CA GLY 1 1.612 -0.031 0.000 1.00 0.00 ATOM 3 C GLY 1 1.985 1.432 0.000 1.00 0.00 ATOM 4 O GLY 1 1.137 2.319 0.000 1.00 0.00 ATOM 5 1H GLY 1 -0.299 -1.179 0.000 1.00 0.00 ATOM 6 2H GLY 1 -0.513 0.641 0.000 1.00 0.00 ATOM 7 1HA GLY 1 2.055 -0.519 0.888 1.00 0.00 ATOM 8 2HA GLY 1 2.055 -0.519 -0.888 1.00 0.00 ATOM 9 HC GLY 1 3.052 1.653 0.000 1.00 0.00

File Import

CrystalMaker imports comments, author information, etc. and displays these in the notebook window. Because only orthogonal coordinates for a single molecule are listed-and not the asymmetric unit, CrystalMaker treats the resulting structure as a Molecule, not a crystal. Any crystallographic information contained in the PDB file is ignored, and we plot the molecule (including both ATOM and HETATOM cards) "as is".

Automatic Bond Generation

CrystalMaker will search out, and plot, nearest-neighbour bonds in the molecule. Bonds are detected if two atoms lie within 15% of the sum of their radii, i.e., the maximum bond distance allowed for two atoms with radii rA and rB is 1.15 (rA+rB).

CrystalMaker uses its default atomic radii in order to determine the bonding pattern. It is therefore essential to ensure that you are using the appropriate set of radii before you import a PDB file! You can use the Elements dialog to check the radii. We suggest that you might wish to import the CSD default radii table, or one of the Covalent radii tables.

Having found nearest-neighbour radii, CrystalMaker also constructs the corresponding bond specification cards, so that you can edit the bonding using the Edit Bond Specifications dialog.

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