Temperature value: Difference between revisions

Line 6:

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.

Temperature value: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

Revision as of 00:03, 27 June 2008 view source Eric Martz (talk \| contribs) ConfirmAccount, Editor, Print3D, Tester, journal, Administrators 30,118 edits created		Revision as of 00:03, 27 June 2008 view source Eric Martz (talk \| contribs) ConfirmAccount, Editor, Print3D, Tester, journal, Administrators 30,118 edits adding content Newer edit →
Line 6:		Line 6:


	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.		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.		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.