Import PDB File
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Import Protein Data Bank (PDB) Files

See the Import File dialog for general aspects of importing atomic-structure data files.

These files can be imported and displayed in all the methods available in ATOMS, i.e. as ball-and-stick, interpenetrating (space-filling) and even polyhedra. ATOMS supports one protein-specific Model mode, the Protein mode, which displays the bonds between the backbone atoms of the amino acids as skeletal cylinders, omitting other atoms in the amino acids (although individual amino acids or residues can be selected for complete plotting in the Protein Display Attributes dialog in the Input2 menu).

Other specialized programs such as RASMOL can display protein structures faster and with more protein-specific options. However, ATOMS may have an advantage over some of these programs in the quality and flexibility of the printed output, for example in using the full resolution of the printer, either directly or as EPS files, Metafiles or PICT files.

Importing PDB files as Crystals. ATOMS can use the information in the SCALEn lines (Cartesian to crystal transformation matrix) and the CRYST1 line to recover the fractional coordinates and space-group symmetry for the original crystal. In some cases this information is not present - if it is present you will be asked if you want to input the data as a crystal instead of a molecule. Note that the transformation matrix given in the SCALEn lines is sometimes not sufficiently precise (because of limitation to 6 places after the decimal point) to recover the original unit-cell parameters (as given in the CRYST1 line) precisely. The cell parameters used in ATOMS are those derived from the transformation matrix, not from the CRYST1 line. After importing, you should check the cell parameters in the Title/Axes dialog and correct the crystal system - because of this problem the cell parameters are always imported as triclinic.

MODEL statements, greater than 99,999 atoms and temperature factors are not supported.

In order to isolate the protein itself, there is an option in the Protein Display Attributes dialog in the Input2 menu which allows omission of all hetatoms, or just water hetatoms. This dialog also sets the parameters for the Protein Model Mode.

ATOMS is able to use the information on residues which is present in the file, as well as CONECT records, to greatly decrease the time required to locate bonds, compared to standard ATOMS methods for crystals. However, if some bonds are missing from the drawing it may be necessary to uncheck the PDB quick bonds box in the Bonds dialog (Input1 menu), and generate a complete set of standard ATOMS bonds.

Connectivity tables. The PDB connectivity or bonding tables, as derived from the CONECT records in the file, are somewhat problematic as there may be conflict with the bond-locating algorithms in ATOMS, and consequent duplication. Currently, on importing a PBD file ATOMS will query if you want to ignore the connectivity tables - unless there is a special reason for keeping the table(s), it is usually best to do so. If you choose to keep the table(s), or in old ATOMS files which always kept the table(s), the properties of bonds in the connectivity table(s) are given as the first item(s) in the Bonds dialog in the Input1 menu. Deleting one of these items deletes the connectivity table.

Doing the Generated to Input conversion (Transform menu), or adding hydrogens (Atoms dialog in the Input1 menu) will automatically delete any connectivity tables.