Electron density maps: Difference between revisions

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Different parts of a crystal structure can show different degrees of order. In a perfect crystal, every asymetric unit would look exactly the same, and not change atomic positions over time. In a real crystal, there is disorder. For example, side chains on the surface of the protein are often disordered (have multiple conformations), while side chains in the hydrophobic core are typically well-ordered (have a single conformation). It is also possible for one domain to be highly ordered (often the biggest domain with many contacts in the crystal) while another is less ordered (e.g. a domain loosely attached to the remainder of the structure).

A highly ordered atom will contribute a sharp peak to the electron density, while a less-ordered atom will contribute a broader and lower peak which is more difficult to distinguish from experimental noise. The atomic displacement parameters model this degree of order (with low values corresponding to ordered atoms and high values corresponding to disordered atoms). Thus by coloring the atomic model by disorder (or ~~temperature~~ factor), you can see which parts of a structure are most highly ordered without actually displaying the electron density. You can also see which parts of the atomic model have high certainty (those in highly-ordered regions with clear electron density) and which were difficult to model appropriately (those in less-ordered regions with features barely rising above the noise). In [[FirstGlance]], in the Tools tab, "Local Uncertainty" colors by temperature factor.

A highly ordered atom will contribute a sharp peak to the electron density, while a less-ordered atom will contribute a broader and lower peak which is more difficult to distinguish from experimental noise. The atomic displacement parameters model this degree of order (with low values corresponding to ordered atoms and high values corresponding to disordered atoms). Thus by coloring the atomic model by disorder (also termed [[temperature factor]] or B factor), you can see which parts of a structure are most highly ordered without actually displaying the electron density. You can also see which parts of the atomic model have high certainty (those in highly-ordered regions with clear electron density) and which were difficult to model appropriately (those in less-ordered regions with features barely rising above the noise). In [[FirstGlance]], in the Tools tab, "Local Uncertainty" colors by temperature factor.

===Fo-Fc Difference Map===

Electron density maps: Difference between revisions

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 Different parts of a crystal structure can show different degrees of order. In a perfect crystal, every asymetric unit would look exactly the same, and not change atomic positions over time. In a real crystal, there is disorder. For example, side chains on the surface of the protein are often disordered (have multiple conformations), while side chains in the hydrophobic core are typically well-ordered (have a single conformation). It is also possible for one domain to be highly ordered (often the biggest domain with many contacts in the crystal) while another is less ordered (e.g. a domain loosely attached to the remainder of the structure).
-A highly ordered atom will contribute a sharp peak to the electron density, while a less-ordered atom will contribute a broader and lower peak which is more difficult to distinguish from experimental noise. The atomic displacement parameters model this degree of order (with low values corresponding to ordered atoms and high values corresponding to disordered atoms). Thus by coloring the atomic model by disorder (or temperature factor), you can see which parts of a structure are most highly ordered without actually displaying the electron density. You can also see which parts of the atomic model have high certainty (those in highly-ordered regions with clear electron density) and which were difficult to model appropriately (those in less-ordered regions with features barely rising above the noise). In [[FirstGlance]], in the Tools tab, "Local Uncertainty" colors by temperature factor.
+A highly ordered atom will contribute a sharp peak to the electron density, while a less-ordered atom will contribute a broader and lower peak which is more difficult to distinguish from experimental noise. The atomic displacement parameters model this degree of order (with low values corresponding to ordered atoms and high values corresponding to disordered atoms). Thus by coloring the atomic model by disorder (also termed [[temperature factor]] or B factor), you can see which parts of a structure are most highly ordered without actually displaying the electron density. You can also see which parts of the atomic model have high certainty (those in highly-ordered regions with clear electron density) and which were difficult to model appropriately (those in less-ordered regions with features barely rising above the noise). In [[FirstGlance]], in the Tools tab, "Local Uncertainty" colors by temperature factor.
 ===Fo-Fc Difference Map===