6CYANA: distances modify - CYANA command

Parameters: pseudoonly

This command modifies distance restraints. Distance limits with
diastereotopic groups are adjusted and/or pseudo atoms are inserted
if no stereospecific assignment is available. Unless the option
'pseudoonly' is set, redundant and meaningless distance restraints
are removed, too.

This command cannot be used for ambiguous distance restraints.

A detailed report of the modifications made is provided if the
information level is full ('info=full'). A first table reports the
modifications made to make distance restraints symmetric under the
exchange of diastereotopic partners in order to account for the
absence of stereospecific assignments. For example:

  Modifications for floating stereospecific assignments:

        Atom(s) A      Atom(s) B      Input restraint(s)      modified to
                                      A1-B1 A1-B2 A2-B1 A2-B2 Ai-Bj QA-QB
  Upper HA     ASP 1 - HD2/3  PRO  2        3.39              3.55
  Upper HB2/3  ASP 1 - HD2/3  PRO  2  5.50  5.50  3.89  5.41  5.50  4.97
  Upper HB2    PRO 2 - HG2/3  MET  3  5.50                          6.38
  Upper HD2/3  PRO 2 - QE     TYR 19  7.63                          8.51
  Upper H      MET 3 - HB2/3  MET  3  3.95  3.33              3.83  3.45
  Upper HB2/3  MET 3 - QE     MET  3  6.53        6.31        6.53
  Upper HB2/3  MET 3 - H      THR  4  5.38        5.50        5.50
  Upper HB2/3  MET 3 - HA     THR  4  4.69                          5.54
  Upper HG2/3  MET 3 - H      THR  4  4.14                          5.01
  Upper HG2/3  MET 3 - HB     THR  4              5.50              6.38
  Upper HG2/3  MET 3 - QB     ALA  8              6.53              7.40
  Upper HG2/3  MET 3 - QD     TYR 19  7.64                          8.52
  Upper HG2/3  MET 3 - QE     TYR 19  7.63                          8.51
  Upper QE     MET 3 - HG2/3  MET 16  5.47                          6.35
  Upper QG2    THR 4 - HE21/2 GLN  7  6.53                          7.39
  Upper H      GLU 6 - HG2/3  GLU  6  5.04  5.50              5.50  5.14

Each line in the listing of distance restraint modifications treats a
pair of distance restraints in case one diastereotopic pair (without
stereospecific assignment) is involved, or a group of up to four of
distance restraints in case two diastereotopic pairs are involved. The
input restraints are listed in the columns A1-B1, A1-B2, A2-B1 and
A2-B2, where A1 denotes the first atom of the first diastereotopic
group, A2 the second atom of the first diastereotopic group, B1 the
first atom of the second diastereotopic group, and B2 the second atom
of the second diastereotopic group.

These will then be replaced by the distance restraints listed in the
two columns Ai-Bj and QA-QB. A number in the Ai-Bj column indicates
that equal distance restraints with this upper bound are applied to
all two or four individual distances that involve the diastereotopic
substituents. A number given in the QA-QB column indicates the single
upper distance bound that is applied to the distance to the pseudoatom,
or between the two pseudoatoms in the case of two prochiral groups.

A second table reports redundant and meaningless restraints that
are removed.  For example:

  Meaningless distance restraints:
                                       limit  diagnosis
  Upper HA    ASP   1 - HB3   ASP   1   3.21  duplicate restraint
  Upper HA    ASP   1 - HB3   ASP   1   3.21  no restriction
  Upper HA    ASP   1 - HD2   PRO   2   4.20  duplicate restraint
  Upper HA    ASP   1 - HD2   PRO   2   4.20  no restriction
  Upper HA    ASP   1 - HD3   PRO   2   3.21  duplicate restraint
  Upper HB2   ASP   1 - HB3   ASP   1   2.40  duplicate restraint
  Upper HB2   ASP   1 - HB3   ASP   1   2.40  fixed distance
  Upper HB2   ASP   1 - HD2   PRO   2   5.50  duplicate restraint
  ...
  Number of modified restraints: 597

Distance restraints can be meaningless for one of the following
reasons:

  fixed distance       The restraint concerns an interatomic distance that
                       cannot be varied by changing the rotatable torsion
                       angles. Examples of this sort are restraints between
                       geminal hydrogen atoms, or restraints between atoms
                       of the same aromatic ring.

  no restriction       The restraint is such that there exists no
                       conformation that would violate it. The program
                       can detect this only if the restrained distance
                       depends on one or two dihedral angles.

  duplicate restraint  The same restraint occurs more than once in the
                       input, for instance because transposed peaks were
                       present in the peak list. The most restrictive
                       restraint is kept in this case.

The number of upper distance limits after the modifications is given
at the end of the table. Depending on the number of stereospecific
assignments, the modifications may increase or decrease the number
of restraints.

Further reading:

- Guentert et al. J. Mol. Biol. 217, 517-530 (1991).
- Guentert et al. J. Mol. Biol. 217, 531-540 (1991).

See also: distance multiple, distance unique
