CYANA Commands: 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).