Pseudo Atoms
CARA allows any number of atoms to be associated to a group of spins. During assignment, you can use either the name of the individual spins (HB2, HB3) or the name of the group (QB). In many cases, CARA will check for inconsistent use of labels (e.g. a mix of HB2 and QB), but the final responsibility remains with the user.
The Molecule Viewer can be used to edit an amino acid definition and to define spins to belong to a group. Select the atoms in question and use the context menu. A blue text appears below all group members.
Most amino acids in our CARA templates were constructed such that only pseudo-atoms which could show splittings in real situations are defined as group members. Ala QB is never resolved into 3 different spins, so it is defined as a single spin with magnitude 3.
Note: In the new CARA template Start1.2.cara (see TemplatesPage), pseudoatoms are named differently. You simply drop the number which distinguishes between the members of the pseudoatom set. E.g. ALA methyl group: {HB1, HB2, HB3} Group = HB. This follows BMRB/IUPAC nomenclature.
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