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:

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

• Guntert et al. J. Mol. Biol. 217, 517-530 (1991).
• Guntert et al. J. Mol. Biol. 217, 531-540 (1991).
• Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).