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Peak selections are made with the [[CYANA command: peaks select|peaks 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. Peak selections that contain blanks must be enclosed in double quotes.

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 <math>\textstyle d = \sqrt{\sum_{k=1}^n\left(\frac{\omega_{ik}-\omega_{jk}}{\Delta\omega_k}\right)^2}</math> where ''&omega;<sub>''ik''</sub>'' and ''&omega;<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and &Delta;''&omega;<sub>k</sub>'' is the chemical shift tolerance for dimension ''k'', as defined by the variable [[CYANA variable: tolerance|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:

 **

All assigned peaks:

 "*, *"

All HA-HA peaks:

 "HA, HA"

All peaks with backbone hydrogens (H, HA) of residues 20–50:

 "H HA 20..50, *"

All peaks with a backbone hydrogen (H, HA) of residues 20–50 in the first dimension:

 "H HA 20..50, * ordered"

All peaks between backbone protons of residues 20–50:

 "H HA 20..50, H HA 20..50"

Peaks between side chain amides and methyls:

 "AMIDE - H, METHYL"

Peaks read from a peak list called n15.peaks:

 "** list=n15.peaks"

Peaks read from the second or third peak list:

 "** list=2..3"

Peaks between 4.6 and 4.8 ppm in the second dimension:

 "** ppm2=4.6..4.8

Select randomly 50% of all assigned peaks:

 "*, * fraction=0.5"

Peaks with only long-range assignments:

 "*, * level=5.. multiple=ifall"

The previously selected peaks and peaks with peak numbers 120–130:

 "+ ** numbers=120..130"


The command [[CYANA command: peaks select|peaks select]] can be used with the parameter info=full to check peak selections.
Return to Peak selection.
Retrieved from "https://cyana.org/wiki/Peak_selection"
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