CYANA Command: assign - Revision history

Miki at 11:13, 12 January 2010

2010-01-12T11:13:23Z

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	== Further reading ==		== Further reading ==

	* Herrmann et al. J. Mol. Biol. 319, 209-227 (2002).		* Herrmann et al. J. Mol. Biol. 319, 209-227 (2002). (Note that the algorithm implemented in the 'assign' command differs significantly from the original CANDID algorithm described in this publication.)
	(Note that the algorithm implemented in the 'assign' command differs significantly from the original CANDID algorithm described in this
	publication.)
	* Guntert. Meth. Mol. Biol. 278, 353-378 (2004).		* Guntert. Meth. Mol. Biol. 278, 353-378 (2004).
	* Guntert. Prog. NMR Spectrosc. 43, 105-125 (2003).		* Guntert. Prog. NMR Spectrosc. 43, 105-125 (2003).

Miki at 11:11, 12 January 2010

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	; alignfactor=''real'' :(default: 0.5)		; alignfactor=''real'' :(default: 0.5)
	; matchfactor=<real> (default: 0.5)		; matchfactor=''real'' :(default: 0.5)
	; violation=<real> (default: -1.0)		; violation=''real'' :(default: -1.0)
	; probability=<real> (default: 0.2)		; probability=''real'' :(default: 0.2)
	; quality=<real> (default: 0.5)		; quality=''real'' :(default: 0.5)
	; elasticity=<real range> (default: 1.0..1.0)		; elasticity=''real range'' :(default: 1.0..1.0)
	; confidence=<real> (default: 1.0)		; confidence=''real'' :(default: 1.0)
	; supportweight=<real> (default: 1.0)		; supportweight=''real'' :(default: 1.0)
	; pathlength=<integer> (default: 3)		; pathlength=''integer'' :(default: 3)
	; prefer=<integer> (default: 999999)		; prefer=''integer'' :(default: 999999)
	; interrange=<integer range> (default: 0..)		; interrange=''integer range'' :(default: 0..)
	; unassigned=<real> (default: 0.1)		; unassigned=''real'' :(default: 0.1)
	; noartifact=<string> (default: none)		; noartifact=''string'' :(default: none)
	; short		; short
	; nearest		; nearest
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	== Description ==		== Description ==

	The 'assign' command performs automated assignment of the NOESY cross peaks on the basis of the given chemical shifts, knowledge of		The '''assign''' command performs automated assignment of the NOESY cross peaks on the basis of the given chemical shifts, knowledge of covalently constrained short distances, and the selected 3D conformers, if available. The '''assign''' command is used in the [[CYANA Macro: noeassign\|'''noeassign''']] macro to implement a combined automated NOESY assignment and structure calculation strategy.
	covalently constrained short distances, and the selected 3D conformers, if available. The 'assign' command is used in the 'noeassign' macro
	to implement a combined automated NOESY assignment and structure calculation strategy.

	=== Input data ===		=== Input data ===
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	=== Output data ===		=== Output data ===

	Output data comprises assignments made by the 'assign' command for the peaks that were NOT selected in the input peak lists, as well as a		Output data comprises assignments made by the '''assign''' command for the peaks that were NOT selected in the input peak lists, as well as a report including details on the assignment of each individual peak and a summary table. Peaks that were selected on input are not modified. If peaks are assigned and unselected on input, the report also provides a comparison between the input assignment and the new assignment made by the '''assign''' command that overwrites the input assignment.
	report including details on the assignment of each individual peak and a summary table. Peaks that were selected on input are not modified. If
	peaks are assigned and unselected on input, the report also provides a comparison between the input assignment and the new assignment made
	by the 'assign' command that overwrites the input assignment.

	=== Assignment strategy ===		=== Assignment strategy ===
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	H SER 43 - HA ILE 63 far 0 95 0 - 6.4-9.0		H SER 43 - HA ILE 63 far 0 95 0 - 6.4-9.0
	H ALA 22 - HA ILE 63 far 0 99 0 - 9.9-14.6		H ALA 22 - HA ILE 63 far 0 99 0 - 9.9-14.6
	Violated in 0 structures by 0.00 Å.		Violated in 0 structures by 0.00 A.

	- Line 1: Peak number, peak list, peak position, upper distance bound.		- Line 1: Peak number, peak list, peak position, upper distance bound.
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	- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the ''quality'' cutoff are marked as "low quality", and the peak remains unassigned.		- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the ''quality'' cutoff are marked as "low quality", and the peak remains unassigned.

	- Lines 3-7: Individual assignment possibilities		- Lines 3-6: Individual assignment possibilities
	* Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.		* Flag that indicates the input assignment, if present, by a '''*''' if it is among the used assignments, or by a '''!''' otherwise.
	* First atom, identified by its name, residue name, and residue number		* First atom, identified by its name, residue name, and residue number
	* Flag: '+', used assignment; '-', assignment possibility not used		* Flag: '''+''', used assignment; '''-''', assignment possibility not used
	* Second atom, identified by its name, residue name and number		* Second atom, identified by its name, residue name and number
	* Decision on assignment possibility:		* Decision on assignment possibility:
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	* Minimal and maximal distance in the selected conformers (Angstrom)		* Minimal and maximal distance in the selected conformers (Angstrom)
	* Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):		* Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):
	:; ''real'': covalently constrained distance shorter than ''real'' A.		:; ''real'': covalently constrained distance shorter than ''real'' Å.
	:; ''integer'': peak number of a (symmetrically related) peak with the same assignment		:; ''integer'': peak number of a (symmetrically related) peak with the same assignment
	:; ''integer''/''integer'': numbers of two peaks that relate the two atoms of the present assignment through a third atom		:; ''integer''/''integer'': numbers of two peaks that relate the two atoms of the present assignment through a third atom
	:; ''integer''/''real'': peak with number ''integer'' connects the first atom to a third atom whose distance from the second atom is covalently restrained to be shorter than ''real'' A.		:; ''integer''/''real'': peak with number ''integer'' connects the first atom to a third atom whose distance from the second atom is covalently restrained to be shorter than ''real'' Å.
	:; ''real''/''integer'': peak with number ''integer'' connects the second atom to a third atom whose distance from the first atom is covalently restrained to be shorter than ''real'' A.		:; ''real''/''integer'': peak with number ''integer'' connects the second atom to a third atom whose distance from the first atom is covalently restrained to be shorter than ''real'' Å.
	:; ~''integer'': The peak with number ''integer'' connects two atoms that covalently restrained to be less than x A from the first and second atom of the present assignment possibility, respectively.		:; ~''integer'': The peak with number ''integer'' connects two atoms that covalently restrained to be less than x Å from the first and second atom of the present assignment possibility, respectively.
	For reasons of space, only the first few contributions are printed.		For reasons of space, only the first few contributions are printed.
	An ellipsis "..." followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.		An ellipsis "..." followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.

	- Line 8 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by '+' in lines 3-7) is violated by more than the ''violation'' threshold, and the average size of the violation.		- Line 7 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by '+' in lines 3-6) is violated by more than the ''violation'' threshold, and the average size of the violation.

	=== Covalently constrained distances ===		=== Covalently constrained distances ===
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	The '''assign''' command provides special features for symmetric homodimers that can be defined with the [[CYANA Commands: molecules define\|'''molecules define''']] command. In the case of a homodimer, only assignments with the first atom in the first monomer are made. The corresponding symmetric distance restraint can be added afterwards with the [[CYANA Commands: molecules symmetrize\|'''molecules symmetrize''']] command. Homodimer assignments are restricted to be only intramolecular or only intermolecular for peaks with (XEASY) color codes 8 or 9, respectively. Furthermore, intermolecular homodimer assignments between residues ''i'' and ''j'' are considered only if \|''i'' - ''j''\| is within the ''interrange''. Intermolecular assignments of a peak are also excluded if the peak has at least one intramolecular assignment between residues ''i'' and ''j'' with \|''i'' - ''j''\| smaller than the parameter ''prefer''.		The '''assign''' command provides special features for symmetric homodimers that can be defined with the [[CYANA Commands: molecules define\|'''molecules define''']] command. In the case of a homodimer, only assignments with the first atom in the first monomer are made. The corresponding symmetric distance restraint can be added afterwards with the [[CYANA Commands: molecules symmetrize\|'''molecules symmetrize''']] command. Homodimer assignments are restricted to be only intramolecular or only intermolecular for peaks with (XEASY) color codes 8 or 9, respectively. Furthermore, intermolecular homodimer assignments between residues ''i'' and ''j'' are considered only if \|''i'' - ''j''\| is within the ''interrange''. Intermolecular assignments of a peak are also excluded if the peak has at least one intramolecular assignment between residues ''i'' and ''j'' with \|''i'' - ''j''\| smaller than the parameter ''prefer''.

			== Further reading ==

			* Herrmann et al. J. Mol. Biol. 319, 209-227 (2002).
			(Note that the algorithm implemented in the 'assign' command differs significantly from the original CANDID algorithm described in this
			publication.)
			* Guntert. Meth. Mol. Biol. 278, 353-378 (2004).
			* Guntert. Prog. NMR Spectrosc. 43, 105-125 (2003).
			* Jee & Guntert. J. Struct. Funct. Genom. 4, 179-189 (2003).

	== See also ==		== See also ==

Miki at 10:45, 12 January 2010

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	== Parameters ==		== Parameters ==

	; alignfactor=<real> :(default: 0.5)		; alignfactor=''real'' :(default: 0.5)
	; matchfactor=<real> (default: 0.5)		; matchfactor=<real> (default: 0.5)
	; violation=<real> (default: -1.0)		; violation=<real> (default: -1.0)

Miki at 10:45, 12 January 2010

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	== Parameters ==		== Parameters ==

	; alignfactor=<real> (default: 0.5)		; alignfactor=<real> :(default: 0.5)
	; matchfactor=<real> (default: 0.5)		; matchfactor=<real> (default: 0.5)
	; violation=<real> (default: -1.0)		; violation=<real> (default: -1.0)

Miki at 10:44, 12 January 2010

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	- Line 1: Peak number, peak list, peak position, upper distance bound.		- Line 1: Peak number, peak list, peak position, upper distance bound.

	- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the <quality> cutoff are marked as "low quality", and the peak remains unassigned.		- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the ''quality'' cutoff are marked as "low quality", and the peak remains unassigned.

	- Lines 3-7: Individual assignment possibilities		- Lines 3-7: Individual assignment possibilities
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	* Second atom, identified by its name, residue name and number		* Second atom, identified by its name, residue name and number
	* Decision on assignment possibility:		* Decision on assignment possibility:
	:; OK: good assignment with probability above the <probability> cutoff		:; OK: good assignment with probability above the ''probability'' cutoff
	:; far: structure based probability too low		:; far: structure based probability too low
	:; lone: network anchoring based probability too low		:; lone: network anchoring based probability too low
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	* Minimal and maximal distance in the selected conformers (Angstrom)		* Minimal and maximal distance in the selected conformers (Angstrom)
	* Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):		* Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):
	:; <real>: covalently constrained distance shorter than <real> A.		:; ''real'': covalently constrained distance shorter than ''real'' A.
	:; <integer>: peak number of a (symmetrically related) peak with the same assignment		:; ''integer'': peak number of a (symmetrically related) peak with the same assignment
	:; <integer>/<integer>: numbers of two peaks that relate the two atoms of the present assignment through a third atom		:; ''integer''/''integer'': numbers of two peaks that relate the two atoms of the present assignment through a third atom
	:; <integer>/<real>: peak with number <integer> connects the first atom to a third atom whose distance from the second atom is covalently restrained to be shorter than <real> A.		:; ''integer''/''real'': peak with number ''integer'' connects the first atom to a third atom whose distance from the second atom is covalently restrained to be shorter than ''real'' A.
	:; <real>/<integer>: peak with number <integer> connects the second atom to a third atom whose distance from the first atom is covalently restrained to be shorter than <real> A.		:; ''real''/''integer'': peak with number ''integer'' connects the second atom to a third atom whose distance from the first atom is covalently restrained to be shorter than ''real'' A.
	:; ~<integer>: The peak with number <integer> connects two atoms that covalently restrained to be less than x A from the first and second atom of the present assignment possibility, respectively.		:; ~''integer'': The peak with number ''integer'' connects two atoms that covalently restrained to be less than x A from the first and second atom of the present assignment possibility, respectively.
	For reasons of space, only the first few contributions are printed.		For reasons of space, only the first few contributions are printed.
	An ellipsis "..." followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.		An ellipsis "..." followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.

	- Line 8 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by '+' in lines 3-7~~) is violated by more than the <violation> threshold, and the average size of the violation.~~		- Line 8 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by '+' in lines 3-7) is violated by more than the ''violation'' threshold, and the average size of the violation.





	~~The contents of the assignment report is as follows:~~

	~~Line 1: Peak number, peak list, peak position, upper distance bound.~~

	Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0...1). Quality values below the ''quality'' cutoff are marked as "low quality", and the peak remains unassigned.

	~~Lines 3–6: Information about individual assignment possibilities:~~

	* Flag that indicates the input assignment, if present, by a '''*''' if it is among the used assignments, or by a '''!''' otherwise.
	* First atom, identified by its name, residue name, and residue number
	* Flag: '''+''', used assignment; '''-''', assignment possibility not used
	* Second atom, identified by its name, residue name and number
	* Decision on assignment possibility:
	~~:; OK : Good assignment with probability above the ''probability'' cutoff.~~
	~~:; far : Structure based probability too low.~~
	~~:; lone : Network anchoring based probability too low.~~
	~~:; poor : Individual probabilities ok but overall probability too low.~~

	:Note that an assignment with “'''OK'''” is not necessarily used when forming a distance restraint from the peak. Even individually good assignments may be discarded because the overall quality of the peak assignments is too low, or because there exist other, much better assignments for the peak.
	* Overall probability for the assignment possibility (%).
	* Probability for match between peak position and chemical shifts (%).
	* Probability for agreement with input structure bundle (%).
	* Probability derived from network anchoring (%).
	* Minimal and maximal distance in the selected conformers (Å).
	* Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):
	~~:;''r'': Covalently constrained distance shorter than ''r'' Å.~~
	~~:;''i'': Peak number of a (symmetrically related) peak with the same assignment.~~
	~~:;''i<sub>1</sub>''/''i<sub>2</sub>'': Numbers of two peaks that relate the two atoms of the present assignment through a third atom.~~
	~~:;''i''/''r'': Peak with number ''i'' connects the first atom to a third atom whose distance from the second atom is covalently restrained to be shorter than ''r'' Å.~~
	~~:;''r''/''i'': Peak with number ''i'' connects the second atom to a third atom whose distance from the first atom is covalently restrained to be shorter than ''r'' Å.~~
	~~:;''~i'': The peak with number ''i'' connects two atoms that are covalently restrained to be less than x Å from the first and second atom of the present assignment possibility, respectively.~~

	:For reasons of space, only the first few contributions are printed. An ellipsis “...” followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.

	~~Line 7 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by ‘+’ in lines 3–6~~) is violated by more than the ''violation'' threshold, and the average size of the violation.

	=== Covalently constrained distances ===		=== Covalently constrained distances ===

	The covalently constrained short distances are normally taken from distance restraints with weight zero, which can be obtained, for instance, by analyzing a bundle of randomized conformers with the [[CYANA Commands: distances short\|'''distances short''']] command, as implemented in the [[CYANA Macro: noeassign\|'''noeassign''']] macro. If no distance restraints with weight zero exist, the short distances are calculated internally from the select conformers (which should be randomized), if available and if ''violation'' ~~parameter~~ is negative, or by an analytical calculation otherwise.		The covalently constrained short distances are normally taken from distance restraints with weight zero, which can be obtained, for instance, by analyzing a bundle of randomized conformers with the [[CYANA Commands: distances short\|'''distances short''']] command, as implemented in the [[CYANA Macro: noeassign\|'''noeassign''']] macro. If no distance restraints with weight zero exist, the short distances
			are calculated internally from the select conformers (which should be randomized), if available and if ''violation'' is negative, or by an analytical calculation otherwise.

	=== Elasticity of upper distance bounds ===		=== Elasticity of upper distance bounds ===

Miki at 10:38, 12 January 2010

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	- Line 1: Peak number, peak list, peak position, upper distance bound.		- Line 1: Peak number, peak list, peak position, upper distance bound.

	- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the <quality> cutoff are marked as "low quality", and the peak remains unassigned.		- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the <quality> cutoff are marked as "low quality", and the peak remains unassigned.

	- Lines 3-7: Individual assignment possibilities		- Lines 3-7: Individual assignment possibilities
	* Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.		* Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.
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	For reasons of space, only the first few contributions are printed.		For reasons of space, only the first few contributions are printed.
	An ellipsis "..." followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.		An ellipsis "..." followed by the total number of contributions in parenthesis indicates that not all contributions with probability greater than 1% are printed.

	- Line 8 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by '+' in lines 3-7) is violated by more than the <violation> threshold, and the average size of the violation.		- Line 8 (last line): Number of conformers in which the upper distance limit of the ambiguous distance restraint formed by the accepted assignments (marked by '+' in lines 3-7) is violated by more than the <violation> threshold, and the average size of the violation.

Miki at 10:37, 12 January 2010

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Miki at 10:33, 12 January 2010

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	- Second atom, identified by its name, residue name and number		- Second atom, identified by its name, residue name and number
	- Decision on assignment possibility:		- Decision on assignment possibility:
	: 'OK', good assignment with probability above the <probability> cutoff		:; 'OK': good assignment with probability above the <probability> cutoff
	: 'far', structure based probability too low		:; 'far', structure based probability too low
	: 'lone', network anchoring based probability too low		:; 'lone', network anchoring based probability too low
	: 'poor', individual probabilities ok but overall probability too low		:; 'poor', individual probabilities ok but overall probability too low
	- Overall probability for the assignment possibility (%)		- Overall probability for the assignment possibility (%)
	- Probability for match between peak position and chemical shifts (%)		- Probability for match between peak position and chemical shifts (%)

Miki at 10:28, 12 January 2010

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	- Line 1: Peak number, peak list, peak position, upper distance bound.		- Line 1: Peak number, peak list, peak position, upper distance bound.
	- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below		- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the <quality> cutoff are marked as "low quality", and the peak remains unassigned.
	the <quality> cutoff are marked as "low quality", and the peak remains unassigned.
	- Lines 3-7: Individual assignment possibilities		- Lines 3-7: Individual assignment possibilities
	- Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.		- Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.

Miki at 10:27, 12 January 2010

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	- Second atom, identified by its name, residue name and number		- Second atom, identified by its name, residue name and number
	- Decision on assignment possibility:		- Decision on assignment possibility:
	:; 'OK', good assignment with probability above the <probability> cutoff		: 'OK', good assignment with probability above the <probability> cutoff
	:; 'far', structure based probability too low		: 'far', structure based probability too low
	:; 'lone', network anchoring based probability too low		: 'lone', network anchoring based probability too low
	:; 'poor', individual probabilities ok but overall probability too low		: 'poor', individual probabilities ok but overall probability too low
	- Overall probability for the assignment possibility (%)		- Overall probability for the assignment possibility (%)
	- Probability for match between peak position and chemical shifts (%)		- Probability for match between peak position and chemical shifts (%)

← Older revision		Revision as of 12:37, 12 January 2010
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	- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the <quality> cutoff are marked as "low quality", and the peak remains unassigned.		- Line 2: Number of used assignments, number of assignment possibilities, overall quality of the peak assignment (0..1). Quality values below the <quality> cutoff are marked as "low quality", and the peak remains unassigned.
	- Lines 3-7: Individual assignment possibilities		- Lines 3-7: Individual assignment possibilities
	- Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.		* Flag that indicates the input assignment, if present, by a '*' if it is among the used assignments, or by a '!' otherwise.
	- First atom, identified by its name, residue name, and residue number		* First atom, identified by its name, residue name, and residue number
	- Flag: '+', used assignment; '-', assignment possibility not used		* Flag: '+', used assignment; '-', assignment possibility not used
	- Second atom, identified by its name, residue name and number		* Second atom, identified by its name, residue name and number
	- Decision on assignment possibility:		* Decision on assignment possibility:
	:; 'OK': good assignment with probability above the <probability> cutoff		:; OK: good assignment with probability above the <probability> cutoff
	:; 'far', structure based probability too low		:; far: structure based probability too low
	:; 'lone', network anchoring based probability too low		:; lone: network anchoring based probability too low
	:; 'poor', individual probabilities ok but overall probability too low		:; poor: individual probabilities ok but overall probability too low
	- Overall probability for the assignment possibility (%)		* Overall probability for the assignment possibility (%)
	- Probability for match between peak position and chemical shifts (%)		* Probability for match between peak position and chemical shifts (%)
	- Probability for agreement with input structure bundle (%)		* Probability for agreement with input structure bundle (%)
	- Probability derived from network anchoring (%)		* Probability derived from network anchoring (%)
	- Minimal and maximal distance in the selected conformers (Angstrom)		* Minimal and maximal distance in the selected conformers (Angstrom)
	- Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):		* Most important individual contributions to the network anchoring based probability, ordered by decreasing size. The number after the equal sign is the probability in percent for the contribution identified in front of the equal sign, as follows (only the first three possibilities appear in the example above):
	:; <real>: covalently constrained distance shorter than <real> A.		:; <real>: covalently constrained distance shorter than <real> A.
	:; <integer>: peak number of a (symmetrically related) peak with the same assignment		:; <integer>: peak number of a (symmetrically related) peak with the same assignment