CYANA Macro: caliba: Difference between revisions
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|Class | |Class | ||
:::|Peaks/restraints | |||
:::|Function | |||
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Revision as of 15:13, 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:
- 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.
Class
| ||
backbone | :::HN/HA - HN/HA,
|
:::V = A / d6 |