CYANA Macro: caliba: Difference between revisions

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== Parameters ==
== Parameters ==


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== Description ==
== Description ==


Calibrates a peak list, i.e. derives upper limit distance restraints from
Calibrate a peak list for a protein, i.e. derive upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints using the method of the former CALIBA program (Güntert et al., 1991a; Güntert et al., 1991b). The possible upper distance limit values are restricted (before applying possible pseudoatom corrections) to a minimal and a maximal value by the system variable [[CYANA Variables: upl_values|'''upl_values''']]. Only peaks with a volume larger than ''vmin'' are considered. Peaks are classified into three calibration classes:  
all assigned peaks and adds them to the list of current distance
* The “backbone” class includes all distance restraints between the backbone amide and α protons that are less than five residues apart from each other. A relationship ''V = A / u<sup>6</sup>'' between the peak volume ''V'' and the upper distance bound ''u'' is assumed.
restraints. Optionally, only peaks with volume larger than ''vmin''
* The “sidechain” class includes all distance restraints that do not belong to one of the other classes. A relationship ''V = B / u<sup>4</sup>'' between the peak volume ''V'' and the upper distance bound ''u'' is assumed.
or from a peak list with given filename (without extension) may be
• The “methyl” class includes all distance restraints that involve a methyl group. A relationship VCu4 between the peak volume V and the upper distance bound u is assumed.
considered. Peaks are classified into three calibration classes:
The parameters A, B, C are either given by the user as Abb, Bsc and Cmethyl, or calculated automatically as follows: The function calscale is used to calculate A by assuming an average distance avedis for all restraints in the class “backbone”. By default, the scalar B is set to  , where dmin is the minimal upper distance bound given by the system variable upl_values, and C is set to B/3 (Mumenthaler et al., 1997). Optionally, a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be created.
 
  Class        Peaks/restraints               Function
  backbone     HN/HA - HN/HA,                  V = A/d^6
              HN/HA - HA (|i-j| '' 5)
  sidechain    not "backbone" and not "methyl"  V = B/d^4
  methyl      all involving methyl groups      V = C/d^4
 
The parameters A, B and C are either given by the user (A = ''bb'', B = ''sc'',
C = ''methyl''), or calculated automatically using the function '''calscale''' to
determine A by assuming an average distance ''avedis'' for the restraints in the  
class "backbone" and setting B = A/upl_values(1) and C = B/3.
 
Optionally, the resulting distance restraints may be given a relative
''weight'', and a logarithmic plot of volumes versus corresponding minimal  
distances in the selected structures can be written.
 
Further reading:
 
* Guntert et al. J. Mol. Biol. 217, 517-530 (1991).
* Guntert et al. J. Mol. Biol. 217, 531-540 (1991).
* Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).

Revision as of 14:17, 6 August 2009

Parameters

vmin=real
(default: 100.0)
bb=real
(default: -1.0)
sc=real
(default: -1.0)
methyl=real
(default: -1.0)
weight=real
(default: 1.0)
avedis=real
(default: 3.4)
plot=filename.ps
(default: none)

Description

Calibrate a peak list for a protein, i.e. derive upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints using the method of the former CALIBA program (Güntert et al., 1991a; Güntert et al., 1991b). The possible upper distance limit values are restricted (before applying possible pseudoatom corrections) to a minimal and a maximal value by the system variable upl_values. Only peaks with a volume larger than vmin are considered. Peaks are classified into three calibration classes:

  • The “backbone” class includes all distance restraints between the backbone amide and α protons that are less than five residues apart from each other. A relationship V = A / u6 between the peak volume V and the upper distance bound u is assumed.
  • The “sidechain” class includes all distance restraints that do not belong to one of the other classes. A relationship V = B / u4 between the peak volume V and the upper distance bound u is assumed.

• The “methyl” class includes all distance restraints that involve a methyl group. A relationship VCu4 between the peak volume V and the upper distance bound u is assumed. The parameters A, B, C are either given by the user as Abb, Bsc and Cmethyl, or calculated automatically as follows: The function calscale is used to calculate A by assuming an average distance avedis for all restraints in the class “backbone”. By default, the scalar B is set to , where dmin is the minimal upper distance bound given by the system variable upl_values, and C is set to B/3 (Mumenthaler et al., 1997). Optionally, a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be created.

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