Peak selection - Revision history

Guentert at 16:59, 18 December 2012

2012-12-18T16:59:21Z

← Older revision		Revision as of 18:59, 18 December 2012
Line 21:		Line 21:
	;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.		;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.		;numbers=''m''..''n'': Peaks 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.		;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.

141.2.137.254 at 10:23, 10 February 2009

2009-02-10T10:23:50Z

← Older revision		Revision as of 12:23, 10 February 2009
Line 1:		Line 1:
	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.		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:		In addition, peak selections may contain one or several of the following conditions:

Admin at 18:00, 29 January 2009

2009-01-29T18:00:02Z

← Older revision		Revision as of 20:00, 29 January 2009
Line 3:		Line 3:
	In addition, peak selections may contain one or several of the following conditions:		In addition, peak selections may contain one or several of the following conditions:

	;colors=''cmin''..''cmax''		;colors=''cmin''..''cmax'': Peaks with XEASY color code (an integer number) between ''cmin'' and ''cmax''.
	:Peaks with XEASY color code (an integer number) between ''cmin'' and ''cmax''.

	;diagonal=''dmin''..''dmax''		;diagonal=''dmin''..''dmax'': Peaks between ''dmin'' and ''dmax'' ppm from the diagonal.
	:Peaks between ''dmin'' and ''dmax'' ppm from the diagonal.

	;fixed: Peaks that are assigned to conformation-independent distances.		;fixed: Peaks that are assigned to conformation-independent distances.

Admin at 17:59, 29 January 2009

2009-01-29T17:59:40Z

← Older revision		Revision as of 19:59, 29 January 2009
Line 3:		Line 3:
	In addition, peak selections may contain one or several of the following conditions:		In addition, peak selections may contain one or several of the following conditions:

	;colors=''cmin''..''cmax'':		;colors=''cmin''..''cmax''
	Peaks with XEASY color code (an integer number) between ''cmin'' and ''cmax''.		:Peaks with XEASY color code (an integer number) between ''cmin'' and ''cmax''.

	;diagonal=''dmin''..''dmax'':		;diagonal=''dmin''..''dmax''
	Peaks between ''dmin'' and ''dmax'' ppm from the diagonal.		:Peaks between ''dmin'' and ''dmax'' ppm from the diagonal.

	;fixed: Peaks that are assigned to conformation-independent distances.		;fixed: Peaks that are assigned to conformation-independent distances.

Admin at 17:59, 29 January 2009

2009-01-29T17:59:19Z

← Older revision		Revision as of 19:59, 29 January 2009
Line 3:		Line 3:
	In addition, peak selections may contain one or several of the following conditions:		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''.		;colors=''cmin''..''cmax'':
	;diagonal=''dmin''..''dmax'': Peaks between ''dmin'' and ''dmax'' ppm from the diagonal.		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.		;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.		;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.		;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''.		;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=''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''.		;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.		;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.		;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.
			;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 ''ω<sub>''ik''</sub>'' and ''ω<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and Δ''ω<sub>k</sub>'' is the chemical shift tolerance for dimension ''k'', as defined by the variable [[CYANA variable: tolerance\|tolerance]].		;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 ''ω<sub>''ik''</sub>'' and ''ω<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and Δ''ω<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''.		;ppm1=''pmin''..''pmax'': Peaks with shift in dimension 1 between ''pmin'' and ''pmax''.

Admin at 17:58, 29 January 2009

2009-01-29T17:58:25Z

← Older revision		Revision as of 19:58, 29 January 2009
Line 1:		Line 1:
	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 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:		In addition, peak selections may contain one or several of the following conditions:

Admin at 17:57, 29 January 2009

2009-01-29T17:57:14Z

← Older revision		Revision as of 19:57, 29 January 2009
Line 1:		Line 1:
	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. In addition, peak selections may contain one or several of the following conditions:		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.

			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''.		;colors=''cmin''..''cmax'': Peaks with XEASY color code (an integer number) between ''cmin'' and ''cmax''.

Admin at 17:56, 29 January 2009

2009-01-29T17:56:54Z

← Older revision		Revision as of 19:56, 29 January 2009
Line 1:		Line 1:
	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:		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. 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''.		;colors=''cmin''..''cmax'': Peaks with XEASY color code (an integer number) between ''cmin'' and ''cmax''.

Admin at 17:55, 29 January 2009

2009-01-29T17:55:47Z

← Older revision		Revision as of 19:55, 29 January 2009
Line 12:		Line 12:
	;numbers=''m''..''n'': Peaks between with peak numbers between m and n.		;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.		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>d = \sqrt{\sum_{k=1}^n\left(\frac{\omega_{ik}-\omega_{jk}}{\Delta\omega_k}\right)^2}</math> where ''ω<sub>''ik''</sub>'' and ''ω<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and Δ''ω<sub>k</sub>'' is the chemical shift tolerance for dimension ''k'', as defined by the variable [[CYANA variable: tolerance\|tolerance]].		;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 ''ω<sub>''ik''</sub>'' and ''ω<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and Δ''ω<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''.		;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''.		;ppm2=''pmin''..''pmax'': Peaks with shift in dimension 2 between ''pmin'' and ''pmax''.

Admin at 17:51, 29 January 2009

2009-01-29T17:51:30Z

← Older revision		Revision as of 19:51, 29 January 2009
Line 12:		Line 12:
	;numbers=''m''..''n'': Peaks between with peak numbers between m and n.		;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.		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>d = \sqrt{\sum_{k=1}^n(\frac{\omega_{ik}-\omega_{jk}}{\Delta\omega_k})^2}</math> where ''ω<sub>''ik''</sub>'' and ''ω<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and Δ''ω<sub>k</sub>'' is the chemical shift tolerance for dimension ''k'', as defined by the variable [[CYANA variable: tolerance\|tolerance]].		;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>d = \sqrt{\sum_{k=1}^n\left(\frac{\omega_{ik}-\omega_{jk}}{\Delta\omega_k}\right)^2}</math> where ''ω<sub>''ik''</sub>'' and ''ω<sub>''jk''</sub>'' are the chemical shift coordinates of the two peaks in dimension ''k'', and Δ''ω<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''.		;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''.		;ppm2=''pmin''..''pmax'': Peaks with shift in dimension 2 between ''pmin'' and ''pmax''.