Temperature value: Difference between revisions

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In [[X-ray crystallography|crystallography]], '''uncertainty''' in the positions of atoms increases with '''disorder''' in the protein crystal. Disorder may have two components, static and dynamic. [[Resolution]] represents the average uncertainty for all atoms. In contrast, the ''temperature value'' (also called ''temperature factor'' or ''B factor'') quantitates the ~~local~~ uncertainty for each atom. At typical resolutions for protein crystals (where ''occupancy'' cannot be distinguished from ''B value''), a high temperature factor reflects a low [[Electron density map|empirical electron density]] for the atom, and ''vice versa''. Generally, a temperature value of less than 30 Å2 signifies confidence in its position, while a temperature value of greater than 60 Å2 signifies disorder<ref>[http://www.proxychem.com/macromolecular_crystallography.html Macromolecular Crystallography] at ProXyChem.com</ref>.

In [[X-ray crystallography|crystallography]], '''uncertainty''' in the positions of atoms increases with '''disorder''' in the protein crystal. Disorder may have two components, static and dynamic. [[Resolution]] represents the average uncertainty for all atoms. In contrast, the ''temperature value'' (also called ''temperature factor'' or ''B factor'') quantitates the uncertainty for each atom. At typical resolutions for protein crystals (where ''occupancy'' cannot be distinguished from ''B value''), a high temperature factor reflects a low [[Electron density map|empirical electron density]] for the atom, and ''vice versa''. Generally, a temperature value of less than 30 Å2 signifies confidence in its position, while a temperature value of greater than 60 Å2 signifies disorder<ref>[http://www.proxychem.com/macromolecular_crystallography.html Macromolecular Crystallography] at ProXyChem.com</ref>.

The temperature value is recorded in the [[atomic coordinate file]]. In the [[PDB_file#PDB_Data_Format|PDB file format]], it is the last numeric value (columns 61-66) in each ATOM and HETATM record. [[#Coloring by Temperature|Coloring by temperature]] is a common way to visualize the uncertainty for each atom.

Temperature value: Difference between revisions

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Revision as of 23:16, 11 October 2011 view source Eric Martz (talk \| contribs) ConfirmAccount, Editor, Print3D, Tester, journal, Administrators 30,118 edits →Definition ← Older edit		Revision as of 15:17, 12 October 2011 view source Eric Martz (talk \| contribs) ConfirmAccount, Editor, Print3D, Tester, journal, Administrators 30,118 edits No edit summary Newer edit →
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	In [[X-ray crystallography\|crystallography]], '''uncertainty''' in the positions of atoms increases with '''disorder''' in the protein crystal. Disorder may have two components, static and dynamic. [[Resolution]] represents the average uncertainty for all atoms. In contrast, the ''temperature value'' (also called ''temperature factor'' or ''B factor'') quantitates the ~~local~~ uncertainty for each atom. At typical resolutions for protein crystals (where ''occupancy'' cannot be distinguished from ''B value''), a high temperature factor reflects a low [[Electron density map\|empirical electron density]] for the atom, and ''vice versa''. Generally, a temperature value of less than 30 Å<sup>2</sup> signifies confidence in its position, while a temperature value of greater than 60 Å<sup>2</sup> signifies disorder<ref>[http://www.proxychem.com/macromolecular_crystallography.html Macromolecular Crystallography] at ProXyChem.com</ref>.		In [[X-ray crystallography\|crystallography]], '''uncertainty''' in the positions of atoms increases with '''disorder''' in the protein crystal. Disorder may have two components, static and dynamic. [[Resolution]] represents the average uncertainty for all atoms. In contrast, the ''temperature value'' (also called ''temperature factor'' or ''B factor'') quantitates the uncertainty for each atom. At typical resolutions for protein crystals (where ''occupancy'' cannot be distinguished from ''B value''), a high temperature factor reflects a low [[Electron density map\|empirical electron density]] for the atom, and ''vice versa''. Generally, a temperature value of less than 30 Å<sup>2</sup> signifies confidence in its position, while a temperature value of greater than 60 Å<sup>2</sup> signifies disorder<ref>[http://www.proxychem.com/macromolecular_crystallography.html Macromolecular Crystallography] at ProXyChem.com</ref>.

	The temperature value is recorded in the [[atomic coordinate file]]. In the [[PDB_file#PDB_Data_Format\|PDB file format]], it is the last numeric value (columns 61-66) in each ATOM and HETATM record. [[#Coloring by Temperature\|Coloring by temperature]] is a common way to visualize the uncertainty for each atom.		The temperature value is recorded in the [[atomic coordinate file]]. In the [[PDB_file#PDB_Data_Format\|PDB file format]], it is the last numeric value (columns 61-66) in each ATOM and HETATM record. [[#Coloring by Temperature\|Coloring by temperature]] is a common way to visualize the uncertainty for each atom.