Resolution - Revision history

Eric Martz: /* Electron Density Map vs. Resolution */

2022-05-16T21:28:37Z

Electron Density Map vs. Resolution

← Older revision		Revision as of 21:28, 16 May 2022
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	==Electron Density Map vs. Resolution==		==Electron Density Map vs. Resolution==
	The '''images at right (top of this page)''' show how the electron density map<ref name="edm">Electron density maps are the results of [[X-ray crystallography]] experiments.</ref><ref name="stills">These are "perfect" electron density maps calculated from the atomic model (R factor = 0.0%, perfect phases and amplitudes, contoured at 1 sigma). Electron density maps based on experimental data would fit the true conformation less well. Because these electron density maps were calculated from an atomic model that lacked hydrogen atoms, the [[Hydrogen in macromolecular models\|electron densities for hydrogen atoms]] that would appear with experimental data at a resolution of 0.5 Å do not appear.</ref> becomes more accurate and detailed as the resolution value decreases from 5.0 Å to 0.5 Å.		The '''images at right (top of this page)''' show how the [[electron density map]]<ref name="edm">Electron density maps are the results of [[X-ray crystallography]] experiments.</ref><ref name="stills">These are "perfect" electron density maps calculated from the atomic model (R factor = 0.0%, perfect phases and amplitudes, contoured at 1 sigma). Electron density maps based on experimental data would fit the true conformation less well. Because these electron density maps were calculated from an atomic model that lacked hydrogen atoms, the [[Hydrogen in macromolecular models\|electron densities for hydrogen atoms]] that would appear with experimental data at a resolution of 0.5 Å do not appear.</ref> becomes more accurate and detailed as the resolution value decreases from 5.0 Å to 0.5 Å.

	The images at right were taken from a movie<ref name='movie'>The movie ([[Image:Resolution_holton.mpeg]]) was created by James Holton at the Advanced Light Source of the Berkeley Laboratory at the University of California. Holton kindly gave explicit permission to use this movie in Proteopedia. The original source was http://ucxray.berkeley.edu/~jamesh/movies.</ref> in which the atomic model and electron density map rock back and forth while the resolution value (uncertainty) increases from 0.5 to 5.0 Å.		The images at right were taken from a movie<ref name='movie'>The movie ([[Image:Resolution_holton.mpeg]]) was created by James Holton at the Advanced Light Source of the Berkeley Laboratory at the University of California. Holton kindly gave explicit permission to use this movie in Proteopedia. The original source was http://ucxray.berkeley.edu/~jamesh/movies.</ref> in which the atomic model and electron density map rock back and forth while the resolution value (uncertainty) increases from 0.5 to 5.0 Å.

Eric Martz: /* Quick Guide */

2022-05-16T18:51:02Z

Quick Guide

← Older revision		Revision as of 18:51, 16 May 2022
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	*~2.2 - 2.8 Å: Shapes of larger sidechains seen.		*~2.2 - 2.8 Å: Shapes of larger sidechains seen.
	*~2.8 - 3.5 Å: Secondary structure & bulky groups seen. Atoms unclear.		*~2.8 - 3.5 Å: Secondary structure & bulky groups seen. Atoms unclear.
	*~3.5 - 4.0 Å: Most [[chains]] traceable~~. Atoms unclear~~. Atoms unclear.		*~3.5 - 4.0 Å: Most [[chains]] traceable. Atoms unclear.
	*~4.0 - 6.0 Å: Some chains traceable. Atoms unclear.		*~4.0 - 6.0 Å: Some chains traceable. Atoms unclear.
	*~6.0 - 8.0 Å: Shapes of [[domains]] at best. Atoms unclear.		*~6.0 - 8.0 Å: Shapes of [[domains]] at best. Atoms unclear.

Eric Martz: /* Quick Guide */

2022-05-16T17:19:24Z

Quick Guide

← Older revision		Revision as of 17:19, 16 May 2022
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	==Quick Guide==		==Quick Guide==
	Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).		Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).
	*<~1.7 Å: Most atoms very clearly seen.		*< ~1.7 Å: Most atoms very clearly seen.
	*~1.7 - 2.2 Å: Many atoms clearly seen.		*~1.7 - 2.2 Å: Many atoms clearly seen.
	*~2.2 - 2.8 Å: Shapes of larger sidechains seen.		*~2.2 - 2.8 Å: Shapes of larger sidechains seen.
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	*~4.0 - 6.0 Å: Some chains traceable. Atoms unclear.		*~4.0 - 6.0 Å: Some chains traceable. Atoms unclear.
	*~6.0 - 8.0 Å: Shapes of [[domains]] at best. Atoms unclear.		*~6.0 - 8.0 Å: Shapes of [[domains]] at best. Atoms unclear.
	*> 8.0 Å: Largest features seen roughly. Atoms unclear.		*> ~8.0 Å: Largest features seen roughly. Atoms unclear.

	Bear in mind that the resolution value represents the "best" (most ordered) parts of a crystal, and that other parts may have poorer quality. The [[temperature value]] for each atom in a crystallographic model indicates the clarity of its electron density map.		Bear in mind that the resolution value represents the "best" (most ordered) parts of a crystal, and that other parts may have poorer quality. The [[temperature value]] for each atom in a crystallographic model indicates the clarity of its electron density map.

Eric Martz: /* Quick Guide */

2022-05-16T17:14:41Z

Quick Guide

← Older revision		Revision as of 17:14, 16 May 2022
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	==Quick Guide==		==Quick Guide==
	Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).		Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).
	*~<1.7 Å: Most atoms very clearly seen.		*<~1.7 Å: Most atoms very clearly seen.
	*~1.7 - 2.2 Å: Many atoms clearly seen.		*~1.7 - 2.2 Å: Many atoms clearly seen.
	*~2.2 - 2.8 Å: Shapes of larger sidechains seen.		*~2.2 - 2.8 Å: Shapes of larger sidechains seen.

Eric Martz: /* Quick Guide */

2022-05-16T17:14:25Z

Quick Guide

← Older revision		Revision as of 17:14, 16 May 2022
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	==Quick Guide==		==Quick Guide==
	Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).		Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).
	*&~~lsim~~;1.7 Å: Most atoms very clearly seen.		*~<1.7 Å: Most atoms very clearly seen.
	*~1.7 - 2.2 Å: Many atoms clearly seen.		*~1.7 - 2.2 Å: Many atoms clearly seen.
	*~2.2 - 2.8 Å: Shapes of larger sidechains seen.		*~2.2 - 2.8 Å: Shapes of larger sidechains seen.

Eric Martz: /* Quick Guide */

2022-05-16T17:13:51Z

Quick Guide

← Older revision		Revision as of 17:13, 16 May 2022
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	==Quick Guide==		==Quick Guide==
	Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).		Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).
	*≤1.7 Å: Most atoms very clearly seen.		*&lsim;1.7 Å: Most atoms very clearly seen.
	*~1.7 - 2.2 Å: Many atoms clearly seen.		*~1.7 - 2.2 Å: Many atoms clearly seen.
	*~2.2 - 2.8 Å: Shapes of larger sidechains seen.		*~2.2 - 2.8 Å: Shapes of larger sidechains seen.

Eric Martz: /* Quick Guide */

2022-05-16T17:12:49Z

Quick Guide

← Older revision		Revision as of 17:12, 16 May 2022
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	==Quick Guide==		==Quick Guide==
	Here is a quick guide for interpreting values of resolution.		Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]).
	*1.2 ~~Å Excellent -- backbone and most sidechains very clear~~. ~~Some [[Hydrogen in macromolecular models\|hydrogens]] may be resolved, see [[Hydrogen in macromolecular models]]~~.		*≤1.7 Å: Most atoms very clearly seen.
	*2.~~5 Å Good~~ -~~- backbone and many~~ sidechains ~~clear~~.		*~1.7 - 2.2 Å: Many atoms clearly seen.
	*3.5 ~~Å OK -- backbone and~~ bulky ~~sidechains mostly clear~~.		*~2.2 - 2.8 Å: Shapes of larger sidechains seen.
	*5.0 ~~Å Poor~~ -- ~~backbone mostly clear~~; ~~sidechains not clear~~.		*~2.8 - 3.5 Å: Secondary structure & bulky groups seen. Atoms unclear.
			*~3.5 - 4.0 Å: Most [[chains]] traceable. Atoms unclear. Atoms unclear.
			*~4.0 - 6.0 Å: Some chains traceable. Atoms unclear.
			*~6.0 - 8.0 Å: Shapes of [[domains]] at best. Atoms unclear.
			*> 8.0 Å: Largest features seen roughly. Atoms unclear.

	Bear in mind that the resolution value represents the "best" (most ordered) parts of a crystal, and that other parts may have poorer quality. The [[temperature value]] for each atom in a crystallographic model indicates the clarity of its electron density map.		Bear in mind that the resolution value represents the "best" (most ordered) parts of a crystal, and that other parts may have poorer quality. The [[temperature value]] for each atom in a crystallographic model indicates the clarity of its electron density map.

Eric Martz: /* See Also */

2021-08-19T22:08:59Z

Eric Martz at 20:28, 16 July 2021

2021-07-16T20:28:35Z

← Older revision		Revision as of 20:28, 16 July 2021
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	<table border=0 align="left" style="padding-right:15px"><tr><td>		<table border=0 align="left" style="padding-right:15px"><tr><td>
	[[Image:Leu425-ala426-temp12-17(av15)-1io1-labeled-300px.png\|~~300px~~]]		[[Image:Leu425-ala426-temp12-17(av15)-1io1-labeled-300px.png\|250px]]
	</td><td>		</td><td>
	Details at <ref>[[Introduction_to_molecular_visualization#Slabbing\|Slabbed]] image from [http://www.bioinformatics.org/molvis/edm/ Electron Density] at 1.0 σ showing Leu425 and Ala426 in [[1io1]]. Temperature factors in those two residues range from 12 to 17, average 15. Separate red atom at right is a water oxygen.</ref>.		Details at <ref>[[Introduction_to_molecular_visualization#Slabbing\|Slabbed]] image from [http://www.bioinformatics.org/molvis/edm/ Electron Density] at 1.0 σ showing Leu425 and Ala426 in [[1io1]]. Temperature factors in those two residues range from 12 to 17, average 15. Separate red atom at right is a water oxygen.</ref>.

Eric Martz at 22:08, 19 May 2019

2019-05-19T22:08:57Z

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	</td></tr></table>		</td></tr></table>

	Structure determination by [[X-ray crystallography]] or [[cryo-electron microscopy]] produces an [[electron density map]] (shown in <font color="#508050"><b>green</b></font>). The atomic model, shown as sticks ~~above~~, is then built, guided by the electron density map.		Structure determination by [[X-ray crystallography]] or [[cryo-electron microscopy]] produces an [[electron density map]] (shown in <font color="#508050"><b>green</b></font>). The atomic model, shown as sticks, is then built, guided by the electron density map.

	In X-ray crystallography, resolution is the smallest distance between crystal lattice planes that is resolved in the diffraction pattern. High numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution.		In X-ray crystallography, resolution is the smallest distance between crystal lattice planes that is resolved in the diffraction pattern. High numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution.

← Older revision		Revision as of 22:08, 19 August 2021
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	==See Also==		==See Also==
	Within Proteopedia:		Within Proteopedia:
			*[[Cryo-EM#Resolution]]
	*[[Temperature_value#Missing_Residues_and_Atoms\|Missing Residues and Atoms]]		*[[Temperature_value#Missing_Residues_and_Atoms\|Missing Residues and Atoms]]
	*[[Temperature value]]		*[[Temperature value]]