Temperature value: Difference between revisions
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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>. Light blue, white, and pink atoms represent the scale of intermediate temperature values. 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 <font color='red'>'''red'''</font> 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. | 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>. Light blue, white, and pink atoms represent the scale of intermediate temperature values. 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 <font color='red'>'''red'''</font> 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. | ||
Comparison of the temperature colors of two separate models is risky, since some methodological issues can bias the temperature factors. There are [[Temperature color schemes|two temperature coloring schemes: absolute and relative]]. In general, high [[Resolution|resolution]] models tend to have fewer red atoms than do models with modest resolution. For example, a <scene name='Temperature_value/1kzk/1'>small HIV protease at 1.1 Angstroms resolution</scene> ([[1kzk]]) has <scene name='Temperature_value/1kzk/2'>few red atoms</scene>, while the <scene name='Temperature_value/1uwb/2'>larger, less compact HIV reverse transcriptase at 3.2 Angstroms resolution</scene> ([[1uwb]]) has <scene name='Temperature_value/1uwb/1'>many red atoms</scene>. (These scenes are colored by ''relative'' temperature.) Also, many of the surface sidechains are missing (due to disorder) in [[1uwb]]. Missing sidechains are labeled '''S-''' in ''FirstGlance in Jmol'' (linked under the molecule on all [[PDB code]]-titled pages in Proteopedia). | |||
Most [[molecular modeling and visualization software]] packages have an option to color by temperature, including [[FirstGlance in Jmol]], which is linked on every page in Proteopedia that is titled with a [[PDB code]]. In [[FirstGlance in Jmol]] (version 1), this option will be found under ''More Views..'', in the section on ''Quality'', as ''Color by Uncertainty''. | Most [[molecular modeling and visualization software]] packages have an option to color by temperature, including [[FirstGlance in Jmol]], which is linked on every page in Proteopedia that is titled with a [[PDB code]]. In [[FirstGlance in Jmol]] (version 1), this option will be found under ''More Views..'', in the section on ''Quality'', as ''Color by Uncertainty''. | ||
