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2009-01-28T23:35:40Z

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== 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]]

CYANA Commands: calibrate - Revision history

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