CYANA Macro: caliba

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.

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 / d²_min , where d_min 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.

Class	Peaks/restraints	Function
backbone	HN/HA - HN/HA, HN/HA - HA (|i - j| < 5)	V = A / d6