CYANA Macro: caliba: Difference between revisions
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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: | 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 | {|border="1" cellpadding="5" cellspacing="0" style="text-align:center" | ||
|Peaks/restraints | |'''Class''' | ||
|Function | |'''Peaks/restraints''' | ||
|'''Function''' | |||
|- | |- | ||
|backbone | |backbone | ||
|HN/HA - HN/HA, | |HN/HA - HN/HA, | ||
HN/HA - HA (|''i'' - ''j''| < 5) | HN/HA - HA (|''i'' - ''j''| < 5) | ||
|''V'' = ''A'' / ''d''<sup>6</sup> | |||
|V = A / d<sup>6</sup> | |||
|- | |- | ||
|sidechain | |sidechain | ||
|not "backbone" and not "methyl" | |not "backbone" and not "methyl" | ||
|V = B / d<sup>4</sup> | |''V'' = ''B'' / ''d''<sup>4</sup> | ||
|- | |- | ||
|methyl | |methyl | ||
|all involving methyl groups | |all involving methyl groups | ||
|V = C / d<sup>4</sup> | |''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. | 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. | 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 16:45, 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).