In the Rendering section, the following choices are available in all of the first three drop-down menus:
|Ball and Stick||Points|
These choices are available in the Backbone menu only:
|Ribbon (solid)||Trace (wireframe)|
For all three “Tube” options, a thicker tube is indicative of more uncertainty with respect to the position of the atom. Temperature factors and occupancies are relative within the PDB file and should not be directly compared to those in other PDB files.
Tube (occupancy) – Draws the tube in proportion to the occupancy measured over time during x-ray crystallography experiments. Occupancy shows the percentage of time that the atom is in the given location, averaged over a time scale. The occupancy value is always between 0 and 1.
Tube (temperature) – Draws the tube in proportion to the temperature factor (B-factor) measured over time during x-ray crystallography experiments. The temperature value is always between 0 and 1. Low B-factors in the hydrophobic center of a molecule usually result in thinner tubes towards the center. Conversely, higher B-factors near the surface, among the outside chains, produce thicker tubes.
Need more help with this?