CYANA Command: calibrate - Revision history

Admin at 12:14, 12 August 2009

2009-08-12T12:14:36Z

← Older revision		Revision as of 14:14, 12 August 2009
Line 1:		Line 1:
	== Parameters ==		== Parameters ==

	; function=''string'' (required)		; function=''string'': (required)
	; weight=''real'': (default: 1.0)		; weight=''real'': (default: 1.0)
	; plot=''filename''.grf: (default: ''none'')		; plot=''filename''.grf: (default: ''none'')

Admin: /* Description */

2009-08-06T13:44:28Z

Description

← Older revision		Revision as of 15:44, 6 August 2009
Line 12:		Line 12:
	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 ~~Macros~~: graf\|'''graf''']] command.		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.

Admin: /* Description */

2009-08-06T13:43:49Z

Description

← Older revision		Revision as of 15:43, 6 August 2009
Line 12:		Line 12:
	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 Macros: graf\|'''graf''']] command.		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 Macros: 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.


	== See also ==		== See also ==

Admin at 13:42, 6 August 2009

2009-08-06T13:42:27Z

@@ Line 1: / Line 1: @@
 == Parameters ==
@@ Line 11: / Line 10: @@
 == Description ==
-Derives upper distance limits from all selected peaks using the
+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''.
-given, monotonically decreasing calibration ''function'' f(d),
+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*).
-where d represents the distance and f(d) the corresponding volume
+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 Macros: graf|'''graf''']] command.
-(for example, "1/d**6"). The minimal and maximal upper limit (before
+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.
 == See also ==

Admin: 1 revision

2009-01-29T11:26:54Z

1 revision

New page

== 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, "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 then these discrete values are used
for 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 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 x 2 = 12,
and the distance bound is increased by d(QQD,HD*) + d(QB,HB*).

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.

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.

== See also ==

* [[upl_values]]
* [[atoms calibrate]]
* [[peaks calibrate]]
* [[peaks simplecal]]