Electron density maps: Difference between revisions
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Examining the correspondence between the published model [[PDB file]] and the electron density map (EDM) provides much clearer insight into the uncertainties in the model than does merely examining the model itself<ref name="silvaggi">PMID 25554228</ref> (see also | Examining the correspondence between the published model [[PDB file]] and the electron density map (EDM) provides much clearer insight into the uncertainties in the model than does merely examining the model itself<ref name="silvaggi">PMID 25554228</ref> (see also | ||
[[Quality assessment for molecular models]]). In addition to examining the entire map ( | [[Quality assessment for molecular models]]). In addition to examining the entire map (2Fo-Fc) it is revealing to examine the ''difference map'' (Fo-Fc), which shows where the model fails to account for the 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. 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. | |||
The agreement between observed electron density and an atom in the model is quantitated in the PDB file as the atom's [[temperature]] (also called "B factor"). Thus by coloring the atomic model by temperature, you can see where the electron density fits well vs. poorly, without actually displaying the electron density. In [[FirstGlance]], in the Tools tab, "Local Uncertainty" colors by temperature. | |||
==Visualizing Electron Density Maps== | ==Visualizing Electron Density Maps== | ||
