InSane: pseudoatoms
InSane generates a pseudoatom for each group of shift equivalent protons.
Two protons are shift equivalent, if (and only if) they
-
have identical chemical shifts,
-
they are attached to atoms with identical chemical shifts, and
-
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:
-
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.
-
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#.
-
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