CYANA Macro: caliba: Difference between revisions

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; weight=''real'': (default: 1.0)
; weight=''real'': (default: 1.0)
; avedis=''real'': (default: 3.4)
; avedis=''real'': (default: 3.4)
; plot=''filename''.ps: (default: ''none'')
; plot=''filename''.ps: (default: ''blank'')


== Description ==
== 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 [[CYANA Variables: upl_values|'''upl_values''']]. Only peaks with a volume larger than ''vmin'' are considered. Peaks are classified into three calibration classes:  
Calibrates a peak list, i.e. derives upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints. Optionally, only peaks with volume larger than ''vmin'' or from a peak list with given filename (without extension) may be 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 / u<sup>6</sup>'' 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 / u<sup>4</sup>'' 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 / u<sup>4</sup>''  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 [[CYANA Functions: calscale|'''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 ''B = A / d<sup>2</sup><sub>min</sub>''  , where ''d<sub>min</sub>'' is the minimal upper distance bound given by the system variable [[CYANA Variables: upl_values|'''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.
{|border="1" cellpadding="5" cellspacing="0" style="text-align:center"
|'''Class'''
|'''Peaks/restraints'''
|'''Function'''
|-
 
|backbone
|HN/HA - HN/HA,
HN/HA - HA (|''i'' - ''j''| < 5)
|''V'' = ''A'' / ''d''<sup>6</sup>
|-
 
|sidechain
|not "backbone" and not "methyl"
|''V'' = ''B'' / ''d''<sup>4</sup>
|-
 
|methyl
|all involving methyl groups
|''V'' = ''C'' / ''d''<sup>4</sup>
|-
|}
         
The parameters ''A'', ''B'', ''C'' are either given by the user (A = ''bb'', B = ''sc'' and C = ''methyl''), or calculated automatically using the function [[CYANA Functions: calscale|'''calscale''']] to determine A by assuming an average distance ''avedis'' for the restraints in the class “backbone” and setting B = A / up1_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 ==
 
* Güntert et al. J. Mol. Biol. 217, 517-530 (1991).
* Güntert et al. J. Mol. Biol. 217, 531-540 (1991).
* Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).

Latest revision as of 15:45, 12 January 2010

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: blank)

Description

Calibrates a peak list, i.e. derives upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints. Optionally, only peaks with volume larger than vmin or from a peak list with given filename (without extension) may be considered. Peaks are classified into three calibration classes:

Class Peaks/restraints Function
backbone HN/HA - HN/HA,

HN/HA - HA (|i - j| < 5)

V = A / d6
sidechain not "backbone" and not "methyl" V = B / d4
methyl all involving methyl groups V = C / d4

The parameters A, B, C are either given by the user (A = bb, B = sc and 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 / up1_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

  • Güntert et al. J. Mol. Biol. 217, 517-530 (1991).
  • Güntert et al. J. Mol. Biol. 217, 531-540 (1991).
  • Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).
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