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Appendix B - AQUA restraint file formats

1. General

The restraint files are line-oriented, giving one restraint per line. Every restraint line starts with a keyword identifier. Lines beginning with # are ignored. In the Aqua routines empty or blank lines force end of reading, and lines starting with an unknown keyword generate an error.

  1. The first line is a title header (not interpreted).

  2. The second line is:

        count NUM type FORMAT MR
    

    where

  3. The third and following lines contain the restraint information in a format that is described below.

Note: the second line is extended compared to the Aqua0.14 format. The restraint format itself has not changed IN THE ABSENCE OF chain identifiers and residue insertion codes.

THE FORMAT FOR DEFINING CHAIN ID'S AND INSERTION CODES IS LIKELY TO CHANGE IN A FUTURE RELEASE.


2. Distance restraint files

A restraint line contains:

    keyword  residue_name  residue_number  atom_name
          ...residue_name  residue_number  atom_name  bound_1  [ bound_2 ]
(The items appear on one line, but for clarity the example uses two lines)

The keyword can be:

   keyword          data                        BOUND_1        BOUND_2
   ======================================================================
    NOEUPP      NOE restraints                 upper bound        n.a.
    NOELOW      NOE restraints                 lower bound        n.a.
    NOEUPLO     NOE restraints                 upper bound    lower bound
    HBUPP       H-bond restraints              upper bound        n.a.
    HBLOW       H-bond restraints              lower bound        n.a.
    HBUPLO      H-bond restraints              upper bound    lower bound
    SSUPP       Disulphide restraints          upper bound        n.a.
    SSLOW       Disulphide restraints          lower bound        n.a.
    SSUPLO      Disulphide restraints          upper bound    lower bound
    DISUPP      Generic distance restraints    upper bound        n.a.
    DISLOW      Generic distance restraints    lower bound        n.a.
    DISUPLO     Generic distance restraints    upper bound    lower bound

The C-format used to write the file in the conversion scripts is:

The Fortran equivalent of this should be (didn't test it):

Note: the format should be treated as field- rather than column-oriented, since chain identifiers and residue insertion codes lead to extra fields being inserted. The extended format is:
    keyword  [CHAIN id]  residue_name  residue_number  [INSERT code]  atom_name
          ...[CHAIN id]  residue_name  residue_number  [INSERT code]  atom_name
          ...bound_1  [ bound_2 ]


3. Torsion angle restraint files

A restraint line contains:

    keyword  residue_name  residue_number  angle_name  bound_high  bound_low

The keyword can only be ANGLE.

The angle names are: PHI, PSI, CHI1, OMEGA etc.

The C-format used to write the file in the qconvr scripts is:

The Fortran equivalent of this should be (didn't test it):

Note: the format should be treated as field- rather than column-oriented, since chain identifiers and residue insertion codes lead to extra fields being inserted. The extended format is:

    keyword  [CHAIN id]  residue_name  residue_number  [INSERT code]
          ...angle_name  bound_high  bound_low


4. Note on residue names

Some programs (e.g. X-PLOR) do not give the residue name in the restraint files. The conversion scripts use UNK in these cases.


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