Talk:Resolution: Difference between revisions

(11 intermediate revisions by one other user not shown)

Line 1:

==ARTICLE REVISED JUNE 15, 2014==

I incorporated most of the suggestions below into a major revision of the article.

[[User:Eric Martz|Eric Martz]] 02:02, 16 June 2014 (IDT)

==Proposed revision V2==

In structure determinations, resolution is the distance corresponding to the smallest observable feature, i.e. if two objects are closer than this distance, they appear as one combined blob rather than two separate objects. For example, because the resolution of the light microscope is limited to roughly the wave length of light (400 nm = 4000 Å), it is not possible to resolve ("see") separate atoms under a microscope (atomic distances are on the order of 1 Å). The resolution of X-ray crystallography is theoretically limited by the wave length of X-rays (also on the order of 1 Å), but in practice, the quality of the available crystals determines resolution. High numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution. A structure determined using data to 1.5 Å would be referred to as a "1.5 Å structure". 2.05 Å is the median resolution for X-ray crystallographic results in the Protein Data Bank (88,701 on May 15, 2014).

==Confusion of high vs. low resolution==

High resolution is characterized by being able to distinguish smaller features, so there is an inverse relationship between the quality of a structure and the length scale given for the resolution. For example, a 1.0 ~~Angstrom~~ structure resolves finer detail than a 4.0 ~~Angstrom~~ structure, so the 1.0 ~~Angstrom~~ structure is said to have higher resolution than the 4.0 ~~Angstrom~~ structure. For non-experts, it would be ~~easier~~ if the terms were fine and rough resolution rather than high and low resolution, but high and low are the established terms in the field.

High resolution is characterized by being able to distinguish smaller features, so there is an inverse relationship between the quality of a structure and the length scale given for the resolution. For example, a 1.0 Å structure resolves finer detail than a 4.0 Å structure, so the 1.0 Å structure is said to have higher resolution than the 4.0 Å structure. For non-experts, it would be less confusing if the terms were fine and rough resolution rather than high and low resolution, but high and low are the established terms in the field.

==Resolution of a reflection vs resolution of a diffraction data set==

Each diffraction spot (i.e. reflection) in a diffraction pattern has a nominal resolution. The higher the diffraction angle (i.e. further from the center of the diffraction image where the incoming X-ray beam would hit), the higher the resolution. In a diffraction experiment, the goal is to collect as many reflections as possible. However, reflections of high resolution are more difficult to measure because the intensity of reflections drops off ~~with~~ at higher diffraction angles (and with that, higher resolution). In a diffraction image, you will see high intensity spots near the center, and more and more faded spots as you move away from the center. The overall resolution of a diffraction data set refers to the resolution range of reflections measured. For example, "data were collected from 20.0 ~~Angstroms~~ to 2.3 ~~Angstroms~~ with an overall completeness of 96.5%" means that most reflections in this range were collected, and the data set would be described in brief as "2.3 A resolution" data set, referring to the high resolution limit of the data collection.

Each diffraction spot (i.e. reflection) in a diffraction pattern has a nominal resolution. The higher the diffraction angle (i.e. further from the center of the diffraction image where the incoming X-ray beam would hit), the higher the resolution. In a diffraction experiment, the goal is to collect as many reflections as possible. However, reflections of high resolution are more difficult to measure because the intensity of reflections drops off at higher diffraction angles (and with that, higher resolution). In a diffraction image, you will see high intensity spots near the center, and more and more faded spots as you move away from the center. The overall resolution of a diffraction data set refers to the resolution range of reflections measured. For example, "data were collected from 20.0 Å to 2.3 Å with an overall completeness of 96.5%" means that most reflections in this range were collected, and the data set would be described in brief as "2.3 Å resolution" data set, referring to the high resolution limit of the data collection.

==Resolution and ~~Disorder~~ ==

==Resolution and crystal quality ==

The resolution of a diffraction pattern depends on how ordered the crystal is. If it is highly ordered (atoms are in defined positions throughout the crystal and over time), the crystal will diffract to high resolution. The more disorder there is (atoms moving over time, or the content of one unit cell different from the next), the lower the resolution of the diffraction image because the intensity of spots drops with increasing disorder. In order to still be able to measure these weak reflections, it is sometimes possible to increase the intensity of the X-rays used in the experiment, increase the exposure time or sensitivity of the detector or increase the size of the crystals.

==Resolution and diffraction data quality==

A well diffracting crystal will yield a high resolution diffraction data. The higher the resolution, the more reflections in the data set. The number of reflections increases with the inverse cube of the resolution, so a 1.0 ~~Angstrom~~ data set has '''eight''' times the number of reflections than a 2.0 ~~Angstrom~~ data set. If you compare a given reflection measured on a well diffracting crystal to one measured on a poorly diffracting crystal, the former will be measured with higher precision (lower error).

A well diffracting crystal will yield a high resolution diffraction data. The higher the resolution, the more reflections in the data set. The number of reflections increases with the inverse cube of the resolution, so a 1.0 Å data set has '''eight''' times the number of reflections than a 2.0 Å data set. If you compare a given reflection measured on a well diffracting crystal to one measured on a poorly diffracting crystal, the former will be measured with higher precision (lower error).

==Resolution and structure quality==

The higher the resolution of the diffraction data, the more measurements are present to base the model on. Also, an increase in resolution means that ~~low resolution reflections were measure~~ with less error than in a corresponding lower quality diffraction data set. As a consequence, the model can be built with ~~less~~ systematic ~~error~~ (such as missing or misplaced atoms) and with less average coordinate error. The coordinate error (how different two models would be based on the same crystals, but independent measurement, model building and refinement) correlates with resolution, but is of a different order of magnitude. It is also influenced by completeness of the data (higher is better), the free R-factor of the refinement (lower is better), and the completeness of the model (higher is better). A typical crystallographic model based on 2.0 ~~Angstrom~~ data has a coordinate error of ~~around~~ 0.2 ~~Angstrom~~. (http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html)

The higher the resolution of the diffraction data, the more measurements are present to base the model on. Also, an increase in resolution means that a given reflection is measured with less error than in a corresponding lower quality diffraction data set. As a consequence, the model can be built with fewer systematic errors (such as missing or misplaced atoms) and with less average coordinate error. The coordinate error (roughly defined as how different two models would be based on the same crystals, but independent measurement, model building and refinement) correlates with resolution, but is of a different order of magnitude. It is also influenced by completeness of the data (higher is better), the free R-factor of the refinement (lower is better), and the completeness of the model (higher is better). A typical crystallographic model based on 2.0 Å data has a coordinate error of less than 0.2 Å. (http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html)

==B-factors and coordinate error==

Disorder in a crystal is reflected in lower resolution of the diffraction data, as described above. Disorder in the coordinates based on that data can be modeled by introducing B-factors for each atom. They model atomic positions being displaced (by an average distance that is related to the B-factor) from an average position (given by the coordinates). There is no direct relationship between B-factor and coordinate error. If we obtain perfect information about the electron density at atomic resolution, we can infer the average position of an atom even if it has a high B-factor (this amounts to finding the center of a fuzzy dilute cloud as opposed to a compact dense cloud). However, there is an indirect relationship: Higher disorder in a crystal results in lower resolution of the diffraction data, resulting in high coordinate errors. At the same time, the average B-factor of the model will be high, reflecting the disorder of the crystal, so overall coordinate error and overall B-factor will be correlated. For individual atoms or regions of the structure with higher disorder, there is a higher chance for systematic errors in building the model, so this correlation of high B-factors and high coordinate errors extends to separate regions of the protein as well (see [http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html], Figure 4 for an example of correlating B-factors with coordinate errors, given specific values for resolution, completeness and free R-factor, which influence coordinate errors as well.)

~~==Resolution and B-factors==~~

~~Disorder of a crystal is reflected in lower resolution of the diffraction data. Disorder in the coordinates based on that data can be modeled by introducing B-factors for each atom.~~

--[[User:Karsten Theis|Karsten Theis]] 19:12, 15 May 2014 (IDT)

==Proposed revision==

Proposed revision for the beginning of this article, after discussion with Keiichi Namba. Comments welcome!

Line 23:

Line 33:

After an [[electron density map]] is calculated and refined with a fitted atomic model, an uncertainty of atomic position is calculated for each atom in the model. These single-atom uncertainties are called the B factors or temperature values of the atoms (see [[Temperature]]).

==Determination of Resolution==

Talk:Resolution: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
+==ARTICLE REVISED JUNE 15, 2014==
+I incorporated most of the suggestions below into a major revision of the article.
+[[User:Eric Martz|Eric Martz]] 02:02, 16 June 2014 (IDT)
+==Proposed revision V2==
+In structure determinations, resolution is the distance corresponding to the smallest observable feature, i.e. if two objects are closer than this distance, they appear as one combined blob rather than two separate objects. For example, because the resolution of the light microscope is limited to roughly the wave length of light (400 nm = 4000 Å), it is not possible to resolve ("see") separate atoms under a microscope (atomic distances are on the order of 1 Å). The resolution of X-ray crystallography is theoretically limited by the wave length of X-rays (also on the order of 1 Å), but in practice, the quality of the available crystals determines resolution. High numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution. A structure determined using data to 1.5 Å would be referred to as a "1.5 Å structure". 2.05 Å is the median resolution for X-ray crystallographic results in the Protein Data Bank (88,701 on May 15, 2014).
 ==Confusion of high vs. low resolution==
-High resolution is characterized by being able to distinguish smaller features, so there is an inverse relationship between the quality of a structure and the length scale given for the resolution. For example, a 1.0 Angstrom structure resolves finer detail than a 4.0 Angstrom structure, so the 1.0 Angstrom structure is said to have higher resolution than the 4.0 Angstrom structure. For non-experts, it would be easier if the terms were fine and rough resolution rather than high and low resolution, but high and low are the established terms in the field.
+High resolution is characterized by being able to distinguish smaller features, so there is an inverse relationship between the quality of a structure and the length scale given for the resolution. For example, a 1.0 Å structure resolves finer detail than a 4.0 Å structure, so the 1.0 Å structure is said to have higher resolution than the 4.0 Å structure. For non-experts, it would be less confusing if the terms were fine and rough resolution rather than high and low resolution, but high and low are the established terms in the field.
 ==Resolution of a reflection vs resolution of a diffraction data set==
-Each diffraction spot (i.e. reflection) in a diffraction pattern has a nominal resolution. The higher the diffraction angle (i.e. further from the center of the diffraction image where the incoming X-ray beam would hit), the higher the resolution. In a diffraction experiment, the goal is to collect as many reflections as possible. However, reflections of high resolution are more difficult to measure because the intensity of reflections drops off with at higher diffraction angles (and with that, higher resolution). In a diffraction image, you will see high intensity spots near the center, and more and more faded spots as you move away from the center. The overall resolution of a diffraction data set refers to the resolution range of reflections measured. For example, "data were collected from 20.0 Angstroms to 2.3 Angstroms with an overall completeness of 96.5%" means that most reflections in this range were collected, and the data set would be described in brief as "2.3 A resolution" data set, referring to the high resolution limit of the data collection.
+Each diffraction spot (i.e. reflection) in a diffraction pattern has a nominal resolution. The higher the diffraction angle (i.e. further from the center of the diffraction image where the incoming X-ray beam would hit), the higher the resolution. In a diffraction experiment, the goal is to collect as many reflections as possible. However, reflections of high resolution are more difficult to measure because the intensity of reflections drops off at higher diffraction angles (and with that, higher resolution). In a diffraction image, you will see high intensity spots near the center, and more and more faded spots as you move away from the center. The overall resolution of a diffraction data set refers to the resolution range of reflections measured. For example, "data were collected from 20.0 Å to 2.3 Å with an overall completeness of 96.5%" means that most reflections in this range were collected, and the data set would be described in brief as "2.3 Å resolution" data set, referring to the high resolution limit of the data collection.
-==Resolution and Disorder ==
+==Resolution and crystal quality ==
 The resolution of a diffraction pattern depends on how ordered the crystal is. If it is highly ordered (atoms are in defined positions throughout the crystal and over time), the crystal will diffract to high resolution. The more disorder there is (atoms moving over time, or the content of one unit cell different from the next), the lower the resolution of the diffraction image because the intensity of spots drops with increasing disorder. In order to still be able to measure these weak reflections, it is sometimes possible to increase the intensity of the X-rays used in the experiment, increase the exposure time or sensitivity of the detector or increase the size of the crystals.
 ==Resolution and diffraction data quality==
-A well diffracting crystal will yield a high resolution diffraction data. The higher the resolution, the more reflections in the data set. The number of reflections increases with the inverse cube of the resolution, so a 1.0 Angstrom data set has '''eight''' times the number of reflections than a 2.0 Angstrom data set. If you compare a given reflection measured on a well diffracting crystal to one measured on a poorly diffracting crystal, the former will be measured with higher precision (lower error).
+A well diffracting crystal will yield a high resolution diffraction data. The higher the resolution, the more reflections in the data set. The number of reflections increases with the inverse cube of the resolution, so a 1.0 Å data set has '''eight''' times the number of reflections than a 2.0 Å data set. If you compare a given reflection measured on a well diffracting crystal to one measured on a poorly diffracting crystal, the former will be measured with higher precision (lower error).
 ==Resolution and structure quality==
-The higher the resolution of the diffraction data, the more measurements are present to base the model on. Also, an increase in resolution means that low resolution reflections were measure with less error than in a corresponding lower quality diffraction data set. As a consequence, the model can be built with less systematic error (such as missing or misplaced atoms) and with less average coordinate error. The coordinate error (how different two models would be based on the same crystals, but independent measurement, model building and refinement) correlates with resolution, but is of a different order of magnitude. It is also influenced by completeness of the data (higher is better), the free R-factor of the refinement (lower is better), and the completeness of the model (higher is better). A typical crystallographic model based on 2.0 Angstrom data has a coordinate error of around 0.2 Angstrom. (http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html)
+The higher the resolution of the diffraction data, the more measurements are present to base the model on. Also, an increase in resolution means that a given reflection is measured with less error than in a corresponding lower quality diffraction data set. As a consequence, the model can be built with fewer systematic errors (such as missing or misplaced atoms) and with less average coordinate error. The coordinate error (roughly defined as how different two models would be based on the same crystals, but independent measurement, model building and refinement) correlates with resolution, but is of a different order of magnitude. It is also influenced by completeness of the data (higher is better), the free R-factor of the refinement (lower is better), and the completeness of the model (higher is better). A typical crystallographic model based on 2.0 Å data has a coordinate error of less than 0.2 Å. (http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html)
+==B-factors and coordinate error==
+Disorder in a crystal is reflected in lower resolution of the diffraction data, as described above. Disorder in the coordinates based on that data can be modeled by introducing B-factors for each atom. They model atomic positions being displaced (by an average distance that is related to the B-factor) from an average position (given by the coordinates). There is no direct relationship between B-factor and coordinate error. If we obtain perfect information about the electron density at atomic resolution, we can infer the average position of an atom even if it has a high B-factor (this amounts to finding the center of a fuzzy dilute cloud as opposed to a compact dense cloud). However, there is an indirect relationship: Higher disorder in a crystal results in lower resolution of the diffraction data, resulting in high coordinate errors. At the same time, the average B-factor of the model will be high, reflecting the disorder of the crystal, so overall coordinate error and overall B-factor will be correlated. For individual atoms or regions of the structure with higher disorder, there is a higher chance for systematic errors in building the model, so this correlation of high B-factors and high coordinate errors extends to separate regions of the protein as well (see [http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html], Figure 4 for an example of correlating B-factors with coordinate errors, given specific values for resolution, completeness and free R-factor, which influence coordinate errors as well.)
-==Resolution and B-factors==
-Disorder of a crystal is reflected in lower resolution of the diffraction data. Disorder in the coordinates based on that data can be modeled by introducing B-factors for each atom.
 --[[User:Karsten Theis|Karsten Theis]] 19:12, 15 May 2014 (IDT)
+==Proposed revision==
 Proposed revision for the beginning of this article, after discussion with Keiichi Namba. Comments welcome!
@@ Line 23: / Line 33: @@
 After an [[electron density map]] is calculated and refined with a fitted atomic model, an uncertainty of atomic position is calculated for each atom in the model. These single-atom uncertainties are called the B factors or temperature values of the atoms (see [[Temperature]]).
 ==Determination of Resolution==