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.
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 4.0Full name of residue. Unused at present.
Short name of residue. Unused at present.
Single letter name of residue. Unused at present.
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).
Atom name
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.
Bond length, from this atom to the previous atom in the tree structure of the residue (as defined in the FAMILY lines).
Valance Angle, between this atom, its parent, and grandparent, as defined in the tree structure of the molecule.
Defines the tree structure of the residue. Each line can be considered of the form
"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.
Each rotatable bond in the residue has an ANGLE entry.
The rotatable bond is that between the specified atom and its parent.
The name of the angle (PHI, PSI, CHI etc.)
One entry for each rotatable bond. The order in which they are specified gives the tree of rotation groups. Unused at present in NMRFx
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.
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.