CYANA Command: calibrate: Difference between revisions
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== Parameters == | == Parameters == | ||
; function=''string'' | ; function=''string'': (required) | ||
; weight=''real'': (default: 1.0) | ; weight=''real'': (default: 1.0) | ||
; plot=''filename''.grf: (default: ''none'') | ; plot=''filename''.grf: (default: ''none'') | ||
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Derives upper distance limits from all selected peaks using the given, monotonically decreasing calibration ''function f''('''d'''), where '''d''' represents the distance and ''f''('''d''') the corresponding volume (for example, '''function=1/d**6'''). The minimal and maximal upper limit (before possible pseudo atom corrections are applied) are given by the first and last value of the variable [[CYANA Variables: upl_values|'''upl_values''']]. A continuous calibration curve is used if the variable [[CYANA Variables: upl_values|'''upl_values''']] has two values. If it has more than two values, then only these discrete values are used as upper limits. Optionally, the resulting distance restraints may be given a relative ''weight''. | Derives upper distance limits from all selected peaks using the given, monotonically decreasing calibration ''function f''('''d'''), where '''d''' represents the distance and ''f''('''d''') the corresponding volume (for example, '''function=1/d**6'''). The minimal and maximal upper limit (before possible pseudo atom corrections are applied) are given by the first and last value of the variable [[CYANA Variables: upl_values|'''upl_values''']]. A continuous calibration curve is used if the variable [[CYANA Variables: upl_values|'''upl_values''']] has two values. If it has more than two values, then only these discrete values are used as upper limits. Optionally, the resulting distance restraints may be given a relative ''weight''. | ||
This command uses a conventional pseudoatom correction approach to handle NOEs with groups of degenerate or not stereospecifically assigned protons: Before calibration, the volumes of peaks assigned to pseudo atoms are divided by the number of protons that they represent. Pseudo atom corrections equal to the distance between the pseudo atom and the hydrogen atom that they represent are added to the upper distance bound obtained by applying the given calibration ''function''. For instance, the volume of a cross peak between a Leu QQD pseudo atom and a Tyr QB pseudo atom is divided by a 6 × 2 = 12, and the distance bound is increased by ''d''(QQD,HD*)+ ''d''(QB,HB*). | This command uses a conventional pseudoatom correction approach to handle NOEs with groups of degenerate or not stereospecifically assigned protons: Before calibration, the volumes of peaks assigned to pseudo atoms are divided by the number of protons that they represent. Pseudo atom corrections equal to the distance between the pseudo atom and the hydrogen atom that they represent are added to the upper distance bound obtained by applying the given calibration ''function''. For instance, the volume of a cross peak between a Leu QQD pseudo atom and a Tyr QB pseudo atom is divided by a 6 × 2 = 12, and the distance bound is increased by ''d''(QQD,HD*)+ ''d''(QB,HB*). | ||
Optionally, a linear or (with the option '''log''') logarithmic plot of the peak volumes versus corresponding average or (with the option '''d<sub>min</sub>''') minimal distances in the selected structures can be produced. Subsequently, the filename.grf plot file can be converted to a Postscript format with the [[CYANA | Optionally, a linear or (with the option '''log''') logarithmic plot of the peak volumes versus corresponding average or (with the option '''d<sub>min</sub>''') minimal distances in the selected structures can be produced. Subsequently, the filename.grf plot file can be converted to a Postscript format with the [[CYANA Macro: graf|'''graf''']] command. | ||
The commands [[CYANA Commands: atoms calibrate|'''atoms calibrate''']], [[CYANA Commands: peaks calibrate|'''peaks calibrate''']] and [[CYANA Commands: peaks simplecal|'''peaks simplecal''']] provide alternative approaches for converting peak volumes into upper distance bounds that are better suited for automated NOESY assignment and the use of ambiguous distance restraints. | The commands [[CYANA Commands: atoms calibrate|'''atoms calibrate''']], [[CYANA Commands: peaks calibrate|'''peaks calibrate''']] and [[CYANA Commands: peaks simplecal|'''peaks simplecal''']] provide alternative approaches for converting peak volumes into upper distance bounds that are better suited for automated NOESY assignment and the use of ambiguous distance restraints. | ||
Latest revision as of 13:14, 12 August 2009
Parameters
- function=string
- (required)
- weight=real
- (default: 1.0)
- plot=filename.grf
- (default: none)
- log
- dmin
- qfactor
Description
Derives upper distance limits from all selected peaks using the given, monotonically decreasing calibration function f(d), where d represents the distance and f(d) the corresponding volume (for example, function=1/d**6). The minimal and maximal upper limit (before possible pseudo atom corrections are applied) are given by the first and last value of the variable upl_values. A continuous calibration curve is used if the variable upl_values has two values. If it has more than two values, then only these discrete values are used as upper limits. Optionally, the resulting distance restraints may be given a relative weight. This command uses a conventional pseudoatom correction approach to handle NOEs with groups of degenerate or not stereospecifically assigned protons: Before calibration, the volumes of peaks assigned to pseudo atoms are divided by the number of protons that they represent. Pseudo atom corrections equal to the distance between the pseudo atom and the hydrogen atom that they represent are added to the upper distance bound obtained by applying the given calibration function. For instance, the volume of a cross peak between a Leu QQD pseudo atom and a Tyr QB pseudo atom is divided by a 6 × 2 = 12, and the distance bound is increased by d(QQD,HD*)+ d(QB,HB*). Optionally, a linear or (with the option log) logarithmic plot of the peak volumes versus corresponding average or (with the option dmin) minimal distances in the selected structures can be produced. Subsequently, the filename.grf plot file can be converted to a Postscript format with the graf command. The commands atoms calibrate, peaks calibrate and peaks simplecal provide alternative approaches for converting peak volumes into upper distance bounds that are better suited for automated NOESY assignment and the use of ambiguous distance restraints.