Temperature value

In crystallography, Uncertainty in the positions of atoms increases with disorder in the protein crystal. Disorder may have two components, static and dynamic. First, some regions of the molecule may adopt different conformations in different copies of the molecule, each molecule's conformation being stable (static disorder). Second, some regions of every copy of the molecule may be subject to thermal motion, meaning vibration about the rest position (Rhodes). Thermal motion is minimized when the crystal is frozen with liquid nitrogen while being irradiated.

Some regions of the molecule may have higher average disorder, and others lower average disorder. Typically, the ends of chains have higher average disorder, and hence their positions are less certain than are residues in the core of a tightly packed domain, where disorder is less.

   In the PDB format, each atom is given not only X, Y, and Z Cartesian coordinates, but two additional values immediately following called "occupancy" and "temperature factor" (also known as the "isotropic B value"). If the end of a chain adopts either of two stable positions with equal probability, each position has 50% occupancy. The temperature factor is provided to quantitate the level of thermal motion. However, these two components of disorder cannot be distinguished with crystal diffraction data alone. Therefore, the occupancy is often given as 1.0 (100%), while the degree of "blur" in the electron density map, representing both components of disorder, is reported in the temperature value. 

   PE's QuickViews COLOR menu offers a Temperature color scheme, in which the range of temperatures is assigned a spectral sequence from blue (low temperature, higher certainty) to red (higher temperature, higher uncertainty). Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning an positions at all, leading to missing residues.