Q atoms

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     In some PDB entries that were determined by NMR, we have the
following types of atoms:

REMARK   7 PSEUDO-ATOMS DESIGNATED AS Q ARE DIMENSIONLESS REFERENCE
REMARK   7 POINTS REPRESENTING A GROUP OF HYDROGEN ATOMS.  THEY ARE
REMARK   7 PLACED IN THE CENTER OF THE POSITIONS OF THE HYDROGEN ATOMS
REMARK   7 THEY REPRESENT.  QA REPRESENTS THE TWO METHYLENE HYDROGEN
REMARK   7 ATOMS OF GLY.  QB, QG, ... REPRESENT BETA, GAMMA, ...
REMARK   7 METHYLENE OR METHYL GROUPS IN THE SIDE CHAINS.  IN CASE OF
REMARK   7 BRANCHES IN THE SIDE CHAINS THE NUMBERS OF THE PSEUDO-ATOMS
REMARK   7 ARE THE SAME AS THE NUMBERS OF THE CARBONS TO WHICH THE
REMARK   7 HYDROGEN ATOMS ARE ATTACHED.

In the mmCIF dictionary there is the following field:

save__atom_site.calc_flag
    _item_description.description
;              A standard code to signal if the site data has been determined
               by diffraction data or calculated from the geometry of
               surrounding sites, or has been assigned dummy coordinates. The
               abbreviation 'c' may be used in place of 'calc'.
;
    _item.name                  '_atom_site.calc_flag'
    _item.category_id             atom_site
    _item.mandatory_code          no
    _item_aliases.alias_name    '_atom_site_calc_flag'
    _item_default.value           d
    _item_type.code               code
     loop_
    _item_enumeration.value
    _item_enumeration.detail      d
                                 'determined from diffraction measurements'
                                  calc
                                 'calculated from molecular geometry'
                                  c
                                 'abbreviation for "calc"'
                                  dum
                                 'dummy site with meaningless coordinates'

It appears to me that the Q-type atoms must appear as atom_site records
because there is no other way to represent them.  The question then arises
of whether an additional flag should be included under
_item_enumeration.detail to identify these Q-type atoms.

                                     Frances C. Bernstein

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