Electron density maps: Difference between revisions
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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. | 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. | ||
===Fo-Fc Difference Map=== | |||
Fo-Fc is a "difference map". It shows where the experimental density and the atomic model disagree. If the atomic model fitted the experimental density perfectly, the difference map would have no densities. Typically, it has negative densities (atoms in the model where there is no electron density, isomesh conventionally colored red) and positive densities (electron density where there is no atom in the model, isomesh typically colored blue or green). The isomesh typically represents the boundaries at ±3 sigma, namely, regions with a substantial level of disagreement. | |||
==Visualizing Electron Density Maps== | ==Visualizing Electron Density Maps== | ||
