Electron density maps: Difference between revisions
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===2Fo-Fc Map=== | ===2Fo-Fc Map=== | ||
2Fo-Fc is two times the observed (experimental) density minus the density calculated from the current atomic model. It shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Likely errors are represented by (i) substantial density containing no atom, or (ii) atoms with little or no density. The isomesh typically represents the boundary at 1 sigma. | 2Fo-Fc is two times the observed (experimental) density minus the density calculated from the current atomic model. It shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Likely errors are represented by (i) substantial density containing no atom, or (ii) atoms with little or no density. The isomesh typically represents the boundary at ''1 sigma''. | ||
Electron density values fill 3-dimensional space of the map (see this [http://www.bioinformatics.org/molvis/edm/ interactive visualization]). The standard deviation of these values, ''sigma'', is used as a unit of electron density. | |||
====Isomesh==== | ====Isomesh==== | ||
An isomesh is an isosurface represented as a mesh. An example is in the figure at the upper right of this page. An isosurface is a surface placed at a specific value of a continuous parameter, so that it represents the boundary between higher and lower values of that parameter. Perhaps a geographic map is a more familiar example, where each [http://wiki.gis.com/wiki/index.php/Isoline isoline] is a contour line joining positions with the same elevation. In an electron density map, an isomesh joins positions with the same electron density. | An isomesh is an isosurface represented as a mesh. An example is in the figure at the upper right of this page. An isosurface is a surface placed at a specific value of a continuous parameter, so that it represents the boundary between higher and lower values of that parameter. Perhaps a geographic map is a more familiar example, where each [http://wiki.gis.com/wiki/index.php/Isoline isoline] is a contour line joining positions with the same elevation. In an electron density map, an isomesh joins positions with the same electron density. | ||
====Temperature==== | ====Temperature==== | ||
