InSane: pseudoatoms


InSane generates a pseudoatom for each group of shift equivalent protons. Two protons are shift equivalent, if (and only if) they

  1. have identical chemical shifts,

  2.  
  3. they are attached to atoms with identical chemical shifts, and

  4.  
  5. they belong to the same residue.
A pseudoatom is generated even if the "group" of shift equivalent protons contains only a single member. No pseudoatoms are generated for protons with unspecified chemical shifts (na fields in the resonance assignment file). Pseudoatoms do not have coordinates, but for display purposes (e.g. in the NMR spectrum peek (sic) and NMR spectrum lines commands) they are assumed to be localized at the average position of the protons in the the pseudoatom group. Pseudoatoms have names, which are generated from proton names:
  1. for a trivial pseudoatom formed by a single proton, the name of the pseudoatom is the short name of the proton (compact combination of residue name and atom name), e.g. F117HB1.

  2.  
  3. for non-trivial pseudoatoms, the last digit(s) in the short proton name is replaced by the X-Plor wild card character # (any number of digits), e.g. V93HG1#, F117HE#.

  4.  
  5. for protons with non-stereospecific resonance assignment, the last digit of the short name is replaced by a t for the down-field or h for the up-field proton, e.g. V109HGt#, G21HAh. The down-field vs. up-field decision is based on the chemical shifts of the heavy atoms to which the protons are connected (or the shifts of the protons, if they are connected to heavy atoms with identical shifts).
Pseudoatom names are used in the NMR spectrum peek and for the annotations of crosspeaks generated by the NMR peaks assign command.



A.Widmer, NIBR/CPC/CSG-SB