Class: ChainStateSet
Defines a set of states that apply to a chain. The ChainStates in a ChainStateSet are mutually exclusive. Their exact nature is defined by the StateSiteType.
ChainStates serve to distinguish Resonances that arise from the same atom in different states of the chain, to describe the State of molecules used for a structure generation, and to define the state (including fast exchange) of a chain under the conditions of a given experiment.
A ChainState only describes the situation for one particular set of alternatives, and implies nothing about others. For example, a molecule with seven prolines in slow cis/trans equilibrium would have seven ChainStateSets. A given resonance could then be described (by linking it to ChainStates) as Pro-47 cis, Pro-112 trans, without implying anything about the state of the remaining five prolines.
stateSetType and ChainState.name are freely changeable, reflecting the fact that the origin of sets of observed resonances is often unknown until a late stage of analysis. Once the precise situation is known, the following procedures should be used where applicable:
stateSetType: cis/trans
ChainState names: cis, trans
Links: to the two atoms that are cis or trans (in the case of peptide bonds to the two alpha carbons of the residues involved).
stateSetType: protonation
ChainState names: protonated, deprotonated
Links: To the proton that is removed on deprotonation.
stateSetType: isotopomer
ChainState names : isotope codes of the relevant isotopes (e.g. 12C, 13C)
Links: To the atom(s) that change isotope.
NB this mechanism only handles atoms of the same type that change in parallel. If the isotope substitution pattern is more complex, is may be necessary to define several ChainStateSets, possibly redefining the ChainStates when the situation has been analysed.
stateSetType: folding
ChainState names: folded, unfolded
Links : to the residues involved in the transition.
stateSetType : conformation
ChainState names: can be chosen freely
Links: to the residues changing conformation.
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Appendix
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