Protein Model Mode
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This mode, which is a 3D Drawing mode only, only works on data imported from PDB files. It displays the bonds between (all) protein backbone atoms as cylinders, with the radius specified in the Protein Display Attributes dialog. By default, other atoms in the amino acids or residues are omitted, but you can specify a limited number of specific residues to draw in the ball-and-stick mode in the Protein Display Attributes dialog. Hetatoms (non-residues) are always drawn as ball-and-stick.

The bonds drawn in this mode must be specified in the Bonds dialog in the Input1 menu. At a minimum to show the backbone there must be carbon-carbon and carbon-nitrogen bonds. Any other bonds among hetatoms and non-backbone atoms in the residues must also be specified. Usually this can be done by selecting automatic bonds.

This mode relies on the atomic labels and residue information derived from PDB files and cannot be used without importing data in that format.

The amino acids or residues are shown in the shapely color scheme as used by RasMol (www.openrasmol.org). This Model mode shows more detail (more atoms) than the "backbone" mode of RasMol because a main objective is to be able to focus on some of the groups of hetatoms and show their bonding to the amino acids when necessary.