Model Attributes: Molecule

Once a model has been chosen in the left side of the Model Panel, clicking the attributes... button in the right side of the panel brings up a window that lists model attributes and allows them to be changed. Molecule-type models are of class Molecule.

The list includes the attributes of the molecule model and selected attributes of its component atoms, bonds, and residues. Descriptions in the dialog are not necessarily identical to the attribute names (used in the code and in various commands).

Molecule Attributes

Component Atom Attributes

Attributes of individual atoms within a molecule model can be set independently. When different atoms within the model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all atoms in the model will be changed accordingly.

Component Bond Attributes

Attributes of individual bonds within a molecule model can be set independently. When different bonds within the model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all bonds in the model will be changed accordingly.

Component Residue Attributes

Attributes of individual residues within a molecule model can be set independently. When different residues within the model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all residues in the model will be changed accordingly.

If the model was read from a PDB file with information preceding the coordinates, there will be a button marked PDB Headers... at the bottom of the attributes panel. Clicking this button displays the information in a separate window. The Record Type Order can be Alphabetical (AUTHOR precedes COMPND, etc.) or PDB (the stereotyped order used by the Protein Data Bank). Either way, lines of the same record type will be shown in their original order.

Model Attributes: MSMSModel
Model Attributes: SurfaceModel and Volume
Model Attributes: VRMLModel and Volume_Model
UCSF Computer Graphics Laboratory / November 2013