CYANA Macro: caliba: Difference between revisions
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== Parameters == | == Parameters == | ||
| Line 8: | Line 7: | ||
; weight=''real'': (default: 1.0) | ; weight=''real'': (default: 1.0) | ||
; avedis=''real'': (default: 3.4) | ; avedis=''real'': (default: 3.4) | ||
; plot=''filename''.ps: (default: '' | ; plot=''filename''.ps: (default: ''blank'') | ||
== Description == | == Description == | ||
Calibrates a peak list, i.e. derives upper limit distance restraints from | 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: | ||
all assigned peaks and adds them to the list of current distance | |||
restraints. Optionally, only peaks with volume larger than ''vmin'' | {|border="1" cellpadding="5" cellspacing="0" style="text-align:center" | ||
or from a peak list with given filename (without extension) may be | |'''Class''' | ||
considered. Peaks are classified into three calibration classes: | |'''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> | |||
|- | |||
The parameters A, B | |methyl | ||
C = ''methyl''), or calculated automatically using the function '''calscale''' to | |all involving methyl groups | ||
determine A by assuming an average distance ''avedis'' for the restraints in the | |''V'' = ''C'' / ''d''<sup>4</sup> | ||
class | |- | ||
|} | |||
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 | 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. | ||
''weight'', and a logarithmic plot of volumes versus corresponding minimal | |||
distances in the selected structures can be written. | |||
Further reading | == 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). | * 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).