Distances modify

distances_modify

Parameters

pseudoonly

Description

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:

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

See also

• distance multiple
• distance unique