Electron density maps: Difference between revisions

(9 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===

Line 38:

[[Image:Edm-3u7z.png|right|225px]]

[[Image:Edm-6vb2.png|right|275px]]

An "all features" map, 2Fo-Fc, is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the ~~expected~~ diffraction data, Fc, in a way that gives the least-biased result). Typically contoured at '''1 sigma''', it shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Ideally, a feature present in the crystal but not yet included in the model will show up with '''half the signal strength''' compared to features present in the crystal and included in the model. Likewise, spurious features included in the model will show up with half signal strength. This difference between real density and 2Fo-Fc density is called model bias, and is related to using the model (and the experimental data) to judge the correctness of the model, a bit of a circular argument.

An "all features" map, 2Fo-Fc, is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the diffraction data calculated from the atomic model, Fc, in a way that gives the least-biased result). Typically contoured at '''1 sigma''', it shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Ideally, a feature present in the crystal but not yet included in the model will show up with '''half the signal strength''' compared to features present in the crystal and included in the model. Likewise, spurious features included in the model will show up with half signal strength. This difference between real density and 2Fo-Fc density is called model bias, and is related to using the model (and the experimental data) to judge the correctness of the model, a bit of a circular argument.

:The '''example at right''' shows the first report, in 2021, of a new kind of covalent protein crosslink, a [[Lysine-cysteine NOS bonds|lysine-cysteine NOS bond]] between the sidechains of the two amino acids in [[6zx4]]<ref>PMID: 33953398</ref>. Crystal structures reported before the recognition of this type of crosslink will have overlooked the oxygen atom, as appears likely the case for [[3u7z]] published in 2011. In contrast, the map shows clearly the absence of an oxygen between the nitrogen and sulfur in [[6vb2]] (similar N-S distances of 2.6-2.7 Å and similar resolutions of 1.3-1.4 Å).

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====Isomesh====

The figures on this page include isomeshes. The isomesh is a mesh representing an isosurface. 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, for example, 1 sigma.

The figures on this page include isomeshes. The isomesh is a mesh representing an isosurface. 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 topographic 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, for example, 1 sigma.

====Disorder and atomic displacment parameters (temperature factors)====

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].

==Examples==

===In Proteopedia===

* [[User:Karsten Theis/Electron density]] explains and illustrates how to display the electron density map for any selected portion of a crystallographic structure, at various sigma levels.

* [[User:Karsten Theis/Electron density]] explains and illustrates how to display the electron density map in Jmol for any selected portion of a crystallographic structure, at various sigma levels.

* Some of the green links in [[Garman lab: Interconversion of lysosomal enzyme specificities]] show electron density maps for ligands.

===Outside of Proteopedia===

*[http://www.bioinformatics.org/molvis/edm/ Electron Density: Cloud vs. Isomesh "Map"] shows a "raw" electron density map with buttons to hide densities below various sigma "noise" levels. It also shows the isomesh at 1.0 sigma, and the atomic model fitted to the isomesh.

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 38: / Line 38: @@
 [[Image:Edm-3u7z.png|right|225px]]
 [[Image:Edm-6vb2.png|right|275px]]
-An "all features" map, 2Fo-Fc, is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the expected diffraction data, Fc, in a way that gives the least-biased result). Typically contoured at '''1 sigma''', it shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Ideally, a feature present in the crystal but not yet included in the model will show up with '''half the signal strength''' compared to features present in the crystal and included in the model. Likewise, spurious features included in the model will show up with half signal strength. This difference between real density and 2Fo-Fc density is called model bias, and is related to using the model (and the experimental data) to judge the correctness of the model, a bit of a circular argument.
+An "all features" map, 2Fo-Fc, is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the diffraction data calculated from the atomic model, Fc, in a way that gives the least-biased result). Typically contoured at '''1 sigma''', it shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Ideally, a feature present in the crystal but not yet included in the model will show up with '''half the signal strength''' compared to features present in the crystal and included in the model. Likewise, spurious features included in the model will show up with half signal strength. This difference between real density and 2Fo-Fc density is called model bias, and is related to using the model (and the experimental data) to judge the correctness of the model, a bit of a circular argument.
 :The '''example at right''' shows the first report, in 2021, of a new kind of covalent protein crosslink, a [[Lysine-cysteine NOS bonds|lysine-cysteine NOS bond]] between the sidechains of the two amino acids in [[6zx4]]<ref>PMID: 33953398</ref>. Crystal structures reported before the recognition of this type of crosslink will have overlooked the oxygen atom, as appears likely the case for [[3u7z]] published in 2011. In contrast, the map shows clearly the absence of an oxygen between the nitrogen and sulfur in [[6vb2]] (similar N-S distances of 2.6-2.7 &Aring; and similar resolutions of 1.3-1.4 &Aring;).
@@ Line 45: / Line 45: @@
 ====Isomesh====
-The figures on this page include isomeshes. The isomesh is a mesh representing an  isosurface. 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, for example, 1 sigma.
+The figures on this page include isomeshes. The isomesh is a mesh representing an  isosurface. 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 topographic 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, for example, 1 sigma.
 ====Disorder and atomic displacment parameters (temperature factors)====
@@ 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==
 ===In Proteopedia===
-* [[User:Karsten Theis/Electron density]] explains and illustrates how to display the electron density map for any selected portion of a crystallographic structure, at various sigma levels.
+* [[User:Karsten Theis/Electron density]] explains and illustrates how to display the electron density map in Jmol for any selected portion of a crystallographic structure, at various sigma levels.
 * Some of the green links in [[Garman lab: Interconversion of lysosomal enzyme specificities]] show electron density maps for ligands.
 ===Outside of Proteopedia===
 *[http://www.bioinformatics.org/molvis/edm/ Electron Density: Cloud vs. Isomesh "Map"] shows a "raw" electron density map with buttons to hide densities below various sigma "noise" levels. It also shows the isomesh at 1.0 sigma, and the atomic model fitted to the isomesh.