Peak selection

Peak selections are made with the peak select command and consist of two atom selections that are separated by a comma. The comma may be omitted if both atom selections consist of a single atom name. In addition, peak selections may contain one or several of the following conditions:

colors=cmin..cmax

Peaks with XEASY color code (an integer number) between cmin and cmax.

diagonal=dmin..dmax

Peaks between dmin and dmax ppm from the diagonal.

fixed Peaks that are assigned to conformation-independent distances.

fraction=p

Select randomly only a fraction p of all peaks that would normally be selected. This option can be useful when simulating peak lists.

levels=m..n

Peaks between residues that are between m and n residues apart.

limit=dmin..dmax

Peaks with distance limit between dmin and dmax.

list=filename

Select only peaks that were read from the peak list with the given filename (with extension).

list=m..n

Peaks that were read from peak lists m to n. Peak lists are numbered 1, 2,... in the order in which they have been read. Instead of a range specification, m..n, it is also possible to specify a single peak list number, m.

multiple=mode

Select individual assignments of an ambiguously assigned peak according to the given mode: multiple=individual selects assignments individually, as if they would belong to separate peaks; multiple=ifany selects all assignments of a peak if at least one assignment matches the selection; multiple=ifall selects all assignments of a peak only if all assignments match the selection; multiple=no selects all peaks that do not have multiple assignments.

numbers=m..n

Peaks between with peak numbers between m and n.

ordered Peaks for which the assignment in dimension 1 matches the first atom selection and the assignment in dimension 2 matches the second atom selection. If this option is not given, the two atom selections can match in any order.

overlap=doverlap

Peaks with a normalized distance to another peak shorter than doverlap. The normalized distance between two peaks, i and j, in an n-dimensional spectrum is defined by

$d={\sqrt {\sum _{k=1}^{n}(\omega _{ik}-\omega _{jk})}}$ where ω_ik and ω_jk are the chemical shift coordinates of the two peaks in dimension k, and Delta_k is the chemical shift tolerance for dimension k, as defined by the variable tolerance.

ppm1=pmin..pmax: Peaks with shift in dimension 1 between pmin and pmax.

ppm2=pmin..pmax: Peaks with shift in dimension 2 between pmin and pmax.

ppm3=pmin..pmax: Peaks with shift in dimension 3 between pmin and pmax.

ppm4=pmin..pmax: Peaks with shift in dimension 4 between pmin and pmax.

quality=qmin..qmax

Peaks with quality factor between qmin and qmax.

volume=Vmin..Vmax

Peaks with volume between Vmin and Vmax.

variable

Peaks that correspond to conformation de¬pendent distances.

Examples

• • # all peaks

"*, *" # assigned peaks "HA, HA" # HA–HA peaks "H HA 20..50, *" # peaks with backbone protons of residues 20–50 "H HA 20..50, * ordered" # peaks with a backbone proton of residues 20–50 # in the first dimension "H HA 20..50, H HA 20..50" # peaks between backbone protons of

1. residues 20–50

"AMIDE - H, METHYL" # peaks between side chain amides and methyls "** list=n15.peaks" # peaks read from peak list n15.peaks "** list=1..3" # peaks read from the second or third peak list "** ppm2=4.6..4.8" # peaks between 4.6 and 4.8 ppm in the second

1. dimension

"*, * fraction=0.5" # 50% of all assigned peaks selected randomly "*, * level=5.. multiple=ifall" # peaks with only long-range assignments "+ ** numbers=120..130" # the previously selected peaks and peaks 120–130 The command peaks select can be used with the parameter info=full to check peak selections.