Assign
Parameters
- alignfactor=real
- (default: 0.5)
- matchfactor=real
- (default: 0.5)
- violation=real
- (default: -1.0)
- probability=real
- (default: 0.2)
- quality=real
- (default: 0.5)
- elasticity=real range
- (default: 1.0..1.0)
- confidence=real
- (default: 1.0)
- supportweight=real
- (default: 1.0)
- prefer=integer
- (default: 999999)
- interrange=integer range
- (default: 0..)
- unassigned=real
- (default: 0.1)
- short
- changevol
Description
- 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.
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/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.
~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.
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.
Covalently contrained 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 distance short command, as implemented in the 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:
When searching for peak assignments the algorithm can adapt individual upper distance bounds in the input peak lists by a factor within the allowed elasticity range. An individual upper bound can be increased if a slight violation of the original upper distance bound can be avoided by the increased distance limit in at least 80% of the conformers. An individual upper bound can be decreased if the actual distances in the input conformers are consistently shorter than the upper distance bound. By default, there is no "elasticity" of the upper distance bounds, i.e. the input distance limits are used without change. If an upper distance is changed, its modified value is indicated in the first line of the report on the assignment of the peak. The additional option changevol can be used to correct peak volumes according to the internal change of the corresponding upper distance bound using an inverse sixth power relationship.
Additional control parameters:
The probability for the chemical shift matching is calculated using the tolerance values multiplied by matchfactor. A smaller matchfactor implies a higher weight for good agreement between the peak coordinates and the chemical shifts. The mutual alignment of peaks is controlled by the variable tolerance, and the probability for network anchoring is calculated using the tolerance values multiplied by alignfactor. A smaller alignfactor implies a higher weight for good mutual alignment between peaks with assignment possibilities to the same atom(s). When calculating the network anchoring probability of a given peak assignment, the probabilities of other aligned peaks may be scaled by a confidence factor between 0 and 1. Chemical shift assignments with an attached chemical shift error larger than the unassigned cutoff are treated as "unassigned" when determining the initial assignment possibilities of peaks: Only one of the two atoms of an assignment may be "unassigned", and, if in addition the short option is set, only short-range assignments for covalently constrained distances are considered.
Symmetric homodimers:
The assign command provides special features for symmetric homodimers that can be defined with the 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 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 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).