InSane: NOESY peak list


At present, Wit!P can only read crosspeak files in Felix [1] Peak File format (default file extension: .xpk), and write crosspeak files in Felix or Sparky [2] format (default extension: .xpk). In Wit!P crosspeak lists are associated with a spectrum, and may be read into the program by the NMR spectrum command

spectrum> peaks read foobar.mat unassigned.xpk
(to read the peak list unassigned.xpk and associate it with the spectrum foobar.mat, which must be a spectrum which was opened with the spectrum open command).

The Felix Peak File format is a fixed format text file, with a two line header, followed by one line per crosspeak. The first header is a comment, which is arbitrary, except that the first three characters must be c**. The second header line contains the 3 letter tag xpk in columns 1-3, followed by the dimension of the spectrum (columns 4-11, right-justified). Crosspeak records contain the following information (example for a 3-dimensional spectrum):

nr  s1 w1 f1 ass1  s2 w2 f2 ass2  s3 w3 f3 ass3  z
(I6, 3(F10.3,F10.3,I6,2X,A16), F10.2)


nr:
Peak number, in ascending order, not necessarily contiguous
si:
Peak position in points, i-th dimension (i = 1...3)
wi:
Peak width in points, i-th dimension (i = 1...3)
fi:
unknown content (i = 1...3)
assi:
assignment field, i-th dimension (i = 1...3)
z:
unknown content

Peak lists may be written to disk files in Felix or Sparky format with the NMR spectrum command, e.g.

spectrum> peaks write foobar.mat felix assigned.xpk
(to write the peaks associated with spectrum foobar.mat in Felix format to the disk file assigned.xpk). On output, the InSane procedure uses the following conventions for the assignment fields assi:

Crosspeak Annotation Conventions:

  1. Text in assignment fields is case sensitive, left justified, w/o blank space (except for trailing blanks).
  2. Assignment fields for dimensions 1&2 contain comma-separated lists of pseudoatom names, or null if no pseudoatom pair is assigned to the peak.
  3. The assignment field for dimension 3 contains the number of pesudoatom pairs assigned to the peak, or null if no pairs are assigned. The pairs assigned to the peak are formed by corresponding pseudoatoms, i.e. 1st pair = 1st atom dim. 1/1st atom dim.2, 2nd pair = 2nd atom/2nd atom, etc. If the first (or second) atom is the same for all pairs assigned to the peak, the corresponding comma separated list of pseudoatom names is reduced to a single name.
  4. A ">" as the last character of the assignment field indicates field overflow (field is too short to hold the complete list of pseudoatom names). Peaks with overflow in any of the assignment fields will not be converted to distance constraints by xpk2xpl.
  5. a "<" as the last character of the assignment text marks a "deleted" peak (c.f. delxpk).



References:

1. http://www.accelrys.com/felix. Commercial NMR data processing, visualization and analysis software from Accelrys.

2. http://www.cgl/ucsf/edu/home/sparky. Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids and other polymers, written by T.D.Goddard and D.G.Kneller, University of California, San Francisco.



A.Widmer, NIBR/CPC/CSG-SB