Electron density maps: Difference between revisions
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[[Image:Plant Physiology 76 175.JPG|thumb|right]] | [[Image:Plant Physiology 76 175.JPG|thumb|right]] | ||
Electron density values fill 3-dimensional space of the map (see this [http://www.bioinformatics.org/molvis/edm/ interactive visualization]). The term "map" is historical; the three-dimensional electron density was plotted on several pages, section by section, with contour lines corresponding to the value of the density at that location. These plots were called a map, in reference to topographical maps. For a paper showing several examples of maps printed in sections and overlayed, see [https://www.pnas.org/content/pnas/72/12/4866.full.pdf a paper on tRNA structure]. | Electron density values fill the 3-dimensional space of the map (see this [http://www.bioinformatics.org/molvis/edm/ interactive visualization]). The term "map" is historical; the three-dimensional electron density was plotted on several pages, section by section, with contour lines corresponding to the value of the density at that location. These plots were called a map, in reference to topographical maps. For a paper showing several examples of maps printed in sections and overlayed, see [https://www.pnas.org/content/pnas/72/12/4866.full.pdf a paper on tRNA structure]. | ||
The standard deviation of all density values, ''sigma'', is used to describe the strength of features in a map. For example, a "3 sigma peak" is a feature that has a density value higher than three sigma over the average value, which typically is set to zero. | The standard deviation of all density values, ''sigma'', is used to describe the strength of features in a map. For example, a "3 sigma peak" is a feature that has a density value higher than three sigma over the average value, which typically is set to zero. | ||
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[[Molecular_modeling_and_visualization_software|Coot]] | [[Molecular_modeling_and_visualization_software|Coot]] | ||
or | or | ||
[[PyMOL]], which require considerable practice to use effectively. | [[PyMOL]], which require considerable practice to use effectively, and offer a great deal of flexibility for model building. | ||
<!--[[Jmol]] | <!--[[Jmol]] | ||
first became capable of displaying electron density maps in January, 2010. | first became capable of displaying electron density maps in January, 2010. | ||
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A much easier way to view electron density maps is to use [http://firstglance.jmol.org FirstGlance in Jmol]. After you load your [[PDB ID]], go to the Tools tab and click ''Density Maps'' for instructions. You can view the interactive 3D map for any residues that you specify, in a single click, without any command language. Any view in FirstGlance, including electron density maps, can be saved as a static image (see examples above on this page), or as an animation ready to drop into Powerpoint. To see examples of such animations in slides, check out [http://tinyurl.com/movingmolecules tinyurl.com/movingmolecules]. | A much easier way to view electron density maps is to use [http://firstglance.jmol.org FirstGlance in Jmol]. After you load your [[PDB ID]], go to the Tools tab and click ''Density Maps'' for instructions. You can view the interactive 3D map for any residues that you specify, in a single click, without any command language. Any view in FirstGlance, including electron density maps, can be saved as a static image (see examples above on this page), or as an animation ready to drop into Powerpoint. To see examples of such animations in slides, check out [http://tinyurl.com/movingmolecules tinyurl.com/movingmolecules]. | ||
{{Template:PDBMapViewers}} | |||
==Examples== | ==Examples== | ||
