Electron density maps: Difference between revisions

(6 intermediate revisions by the same user not shown)

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[[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.

Electron density maps are available for most

Electron density maps are available for '''most'''

[[PDB files]], e.g.

from [https://www.ebi.ac.uk/pdbe/ PDBe]: at the page titled with the entry ID (4 characters), click on Downloads and look for "EDS map" and "EDS difference map". For some ~~structure~~ deposited before 2008, the diffraction data ~~was~~ not deposited and thus the electron density maps are not available. In 2008, the [[wwPDB]] began requiring that the data be deposited along with the model<ref name="2021berman">PMID:33963295</ref>.

from [https://www.ebi.ac.uk/pdbe/ PDBe]: at the page titled with the entry ID (4 characters), click on Downloads and look for "EDS map" and "EDS difference map". For some structures deposited before 2008, the '''diffraction data were not deposited''' and thus the electron density maps are not available. In 2008, the [[wwPDB]] began '''requiring''' that the data be deposited along with the model<ref name="2021berman">PMID:33963295</ref>.

===2Fo-Fc Map===

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[[Molecular_modeling_and_visualization_software|Coot]]

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. Being able to display EDM's in Jmol opens the door to examining EDMs effectively in a web browser, with a user interface (yet to be developed) that requires no specialized software knowledge.

first became capable of displaying electron density maps in January, 2010.

Being able to display EDM's in Jmol opens the door to examining EDMs effectively in a web browser, with a user interface (yet to be developed) that requires no specialized software knowledge.-->

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].

==Examples==

Electron density maps: Difference between revisions

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@@ Line 26: / Line 26: @@
 [[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.
-Electron density maps are available for most
+Electron density maps are available for '''most'''
 [[PDB files]], e.g.
-from [https://www.ebi.ac.uk/pdbe/ PDBe]: at the page titled with the entry ID (4 characters), click on Downloads and look for "EDS map" and "EDS difference map". For some structure deposited before 2008, the diffraction data was not deposited and thus the electron density maps are not available. In 2008, the [[wwPDB]] began requiring that the data be deposited along with the model<ref name="2021berman">PMID:33963295</ref>.
+from [https://www.ebi.ac.uk/pdbe/ PDBe]: at the page titled with the entry ID (4 characters), click on Downloads and look for "EDS map" and "EDS difference map". For some structures deposited before 2008, the '''diffraction data were not deposited''' and thus the electron density maps are not available. In 2008, the [[wwPDB]] began '''requiring''' that the data be deposited along with the model<ref name="2021berman">PMID:33963295</ref>.
 ===2Fo-Fc Map===
@@ Line 67: / Line 67: @@
 [[Molecular_modeling_and_visualization_software|Coot]]
 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. Being able to display EDM's in Jmol opens the door to examining EDMs effectively in a web browser, with a user interface (yet to be developed) that requires no specialized software knowledge.
+first became capable of displaying electron density maps in January, 2010.
+Being able to display EDM's in Jmol opens the door to examining EDMs effectively in a web browser, with a user interface (yet to be developed) that requires no specialized software knowledge.-->
+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==