Temperature value: Difference between revisions
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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. The disorder for each atom is quantitated in its ''temperature value''. | 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. The disorder for each atom is quantitated in its ''temperature value''. | ||
Visualizing relative disorder or uncertainty in atomic positions is done by ''coloring by temperature value''. Atoms with <font color='blue'>'''low temperature values are colored blue'''</font>, while atoms with <font color='red'>'''high temperature values are colored red'''</font>. | Visualizing relative disorder or uncertainty in atomic positions is done by ''coloring by temperature value''. Atoms with <font color='blue'>'''low temperature values are colored blue'''</font>, while atoms with <font color='red'>'''high temperature values are colored red'''</font>. The temperature values themselves are relative, not absolute, and hence the colors are also relative. The most important information from coloring by temperature is to identify the ''red'' residues whose positions are least certain. Their positions should be taken only as rough approximations, and this is especially worth knowing if any residues in areas of special interest are red. | ||
While the temperature colors of two separate models cannot be rigorously compared (since the temperature values themselves are relative, not absolute), high resolution models tend to have fewer red atoms than to models with modest resolution. | |||
Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning any atomic positions at all, leading to '''missing residues'''. ''FirstGlance in Jmol'' (linked beneath the molecule on every [[PDB code]]-titled page in Proteopedia) has a '''Gaps''' button that explains how to detect and visualize missing residues. | Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning any atomic positions at all, leading to '''missing residues'''. ''FirstGlance in Jmol'' (linked beneath the molecule on every [[PDB code]]-titled page in Proteopedia) has a '''Gaps''' button that explains how to detect and visualize missing residues. | ||
