CYANA Command: distances modify: Difference between revisions

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  Upper HN    GLU 6 - HG2/3  GLU  6  5.04  5.50            5.50  5.14
  Upper HN    GLU 6 - HG2/3  GLU  6  5.04  5.50            5.50  5.14
  Upper HA    GLU 6 - HG2/3  GLU  6  4.23
  Upper HA    GLU 6 - HG2/3  GLU  6  4.23


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 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.
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 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.
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   Number of modified restraints: 597
   Number of modified restraints: 597


Distance restraints can be meaningless for one of the following
Distance restraints can be meaningless for one of the following reasons:
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
:; '''fixed distance''' : The restraint concerns an interatomic distance that cannot be varied by changing the rotatable torsion angles. Examples include restraints between geminal hydrogen atoms, or between atoms of the same aromatic ring.
                      conformation that would violate it. The program
:; '''no restriction''' : The restraint is such that no conformation exists that would violate it. The program can detect this only if the restrained distance depends on one or two torsion angles. Many meaningless intraresidual peaks can thus be eliminated.
                      can detect this only if the restrained distance
:; '''duplicate restraint''' : The same restraint occurs more than once in the input, for example because transposed peaks were present in the peak list. Only the most restrictive of these restraints is kept.
                      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
The number of upper distance limits after the modifications is given at the end of the table. Depending on the extent of stereospecific assignments etc., the '''distances modify''' command  may increase or decrease the number of restraints.
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:
Further reading:

Revision as of 14:27, 7 August 2009

Parameters

pseudoonly

Description

Modifies distance restraints. Distance limits with diastereotopic groups are adjusted and/or pseudoatoms 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 (Güntert et al., 1991a; Güntert et al., 1991b). For example: 

Modifications for floating stereospecific assignments:
                                 Input restraint(s) modified to
Atom(s) A            Atom(s) 		B1-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 HN     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 - HN     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 - HN     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   9  	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             7.3
Upper HN     GLU 6 - HG2/3  GLU   6  	5.04  	5.50             	5.50  5.14
Upper HA     GLU 6 - HG2/3  GLU   6  	4.23

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 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. If the modified distance limit(s) would be meaningless, it is discarded and not reported. 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 include restraints between geminal hydrogen atoms, or between atoms of the same aromatic ring.
no restriction
The restraint is such that no conformation exists that would violate it. The program can detect this only if the restrained distance depends on one or two torsion angles. Many meaningless intraresidual peaks can thus be eliminated.
duplicate restraint
The same restraint occurs more than once in the input, for example because transposed peaks were present in the peak list. Only the most restrictive of these restraints is kept.


The number of upper distance limits after the modifications is given at the end of the table. Depending on the extent of stereospecific assignments etc., the distances modify command 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

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