CYANA Macro: caliba: Difference between revisions
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* 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 “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. | 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. | ||
Revision as of 14:24, 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 B = A / d2min , 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.