Residue Template LIbrary

When generating a molecular structure in NMRFx by reading in a sequence file it is necessary to translate the residue names into the set of atoms and bonds that define the molecular topology. To do this, NMRFx, looks at each residue name in the sequence file, and checks to see if a file corresponding to that name with a ".prf" extension exists in the residue library. If an appropriate residue file is not found in the standard directory (specified with the reslib entry in Preferences), then NMRFx can also look in a local residue library directory (specified with the local,reslib entry in Preferences). This is the appropriate place to place your own special .prf files. This way they won't be accidentally deleted when you upgrade to a new version of NMRFx.

If a residue file is found, that file is scanned to extract the topology for that residue. NMRFx works with residues using an internal coordinate system, where the molecular topology is determined by a tree-like structure starting from the first atom in the structure. To properly define the structure then, it is necessary to provide values for the valance angles, dihedral angles, bond distances and connectivity. Most of this information is defined in the ATOM and FAMILY records. The .prf files, which are derived from information originally published by Robson & Osguthorpe (J. Mol. Biol. 132:19-51) are described below. Our original use of .prf files was in our structure calculation program, PEGASUS (Johnson & Sugg, Biochem., 1992, 31,8151-8159). some of the parameters are only relevant to this structure calculation program, and do not need to be absolutely correct to use the .prf file for NMR assignment purposes.

TXT

LNAME Serine
SNAME ser
RCHAR S
ATOM   N      N'   1.32  114.00  -120.0
ATOM   H      H'   1.00  123.00     0.0
ATOM   CA     C1   1.47  123.00   180.0
ATOM   HA     H    1.08  109.47  -120.0
ATOM   CB     C2   1.53  109.47  -121.5
ATOM   HB2    H    1.08  109.47  -120.0
ATOM   HB3    H    1.08  109.47  -120.0
ATOM   OG     O    1.42  109.47     0.0
ATOM   HG     HO   1.00  110.00     0.0
ATOM   C      C'   1.53  109.47   120.0
ATOM   O      O'   1.24  121.00   180.0
FAMILY   -      N      H      CA
FAMILY   N      CA     C      CB     HA
FAMILY   CA     CB     OG     HB3    HB2
FAMILY   CB     OG     HG
FAMILY   CA     C      +      O
ANGLE     CA      PHI 1
ANGLE     CB     CHI1 2
ANGLE     OG     CHI2 6
ANGLE     C       PSI 1
ATREE  CA  CB  C
ATREE  CB  OG
ATREE  OG
ATREE  C  +
PSEUDO QB HB2 HB3
CRAD CA   4.0

LNAME

: Full name of residue. Unused at present.

SNAME

: Short name of residue. Unused at present.

RCHAR

: Single letter name of residue. Unused at present.

ATOM

: Properties of the atoms in the residue. There should be one line for each atom. The line is composed of 6 fields separated by white space (spaces or tabs).

TXT

1.  Atom name

2.  Atom type, which should reference one of the atom types listed
    in the atoms.def file. Used for getting atomic number and energy
    parameters when doing structure calculations.

3.  Bond length, from this atom to the previous atom in the tree
    structure of the residue (as defined in the FAMILY lines).

4.  Valance Angle, between this atom, its parent, and grandparent,
    as defined in the tree structure of the molecule.

5.  Torsion Angle, between this atom, its parent, grandparent, and
    great grandparent (as defined in the tree structure of the
    molecule). The angle for the first "child" atom bonded to a
    given parent, as defined in the FAMILY lines, is an absolute
    torsion angle. The angles for subsequent atoms are relative to
    the previously defined dihedral.

FAMILY

: Defines the tree structure of the residue. Each line can be considered of the form

TXT

"**FAMILY parentAtom thisAtom childAtom1 childAtom2...**".

For example, a line like, "**FAMILY N CA C CB HA**", implies that
the atom **CA**, is bonded to the **N** atom (the parent of **CA**
is **N**), and it has three children, C, CB and HA. If the parent is
specified as "-", then it is a connector atom in the previous
residue. If a child is specified as "+", then it is the connector
atom in the subsequent residue. Child atom names preceded with a
"-", like**-CD2** imply that this child atom will actually be
defined in the tree structure in some other FAMILY entry in the
structure, but that there should be a bond drawn between this child
atom and the main atom of this FAMILY line. This is used to define
bonds that close rings.

ANGLE

: Each rotatable bond in the residue has an ANGLE entry.

TXT

1.  The rotatable bond is that between the specified atom and its
    parent.

2.  The name of the angle (PHI, PSI, CHI etc.)

3.  A number indicating an entry in the file irp.def, which gives
    energy parameters for the intrinsic rotation potential for this
    atom. Only used in structure calculations.

ATREE

: One entry for each rotatable bond. The order in which they are specified gives the tree of rotation groups. Unused at present in NMRFx

PSEUDO

: Mapping of actual atoms in structure to pseudo atom names, "PSEUDO pseudoAtomName atom1 atom2 ...". The pseudo atom position would be at the geometric mean of all the actual atoms that are listed. At present this is only used when reading in constraint files using pseudo atom names (like CYANA .upl files) and is used to translate the pseudo atom name into the set of actual atoms stored in the molecular structure.

CRAD

: This specifies the name of an atom near the center of the residue and the approximate radius of a sphere around the central atom that would encompass all atoms of the residue. Used for accelerating calculation of non-bond contact list. Unused at present in NMRFx.