xpk2xpl


Usage:

xpk2xpl -p peakfile -v volfile [options...]


Options:

--help or -h output help text.
-p peakfile specifies name of crosspeak file.
-v volfile specifies name of volumes file.
-o outfile name of the output constraints file (default: standard output)
-c vol=dist calibration, e.g. 2.2E8=1.8 (default: automatic)
-a accept ambiguous assignments (default: ignore ambig. assignments). This is experimental, use with caution!
-m margin margin to be used in constraints, fraction of calib. dist. (default: 0.1).
-t convert peakfile to readable text format, instead of X-Plor distance constraints file. Text output always goes to standard output.


Description:

The perlscript xpk2xpl creates an X-Plor distance constraints file from an annotated crosspeak list (Felix crosspeak file format). Only peaks with non-truncated annotation fields (last character of 1st and 2nd proton assignment fields is not '>'), which are not delete flagged (last char. of annotation field is not '<'), and for which the assignment of at least one proton is unique, will be used to generate constraints. Peaks with missing or negative volume will be ignored. Equivalent proton pairs will be merged by averaging volumes.

The t and h tags in pseudoatom names in the assignments of peaks which involve atoms with non-stereospecific resonance assignments will be replaced by the X-Plor wild-card character + ("single digit"), and proton pairs which have become equivalent by this operation will be merged into a single constraint by adding volumes.

Automatic calibration: uses all peaks with geminal proton assignments. The distance between geminal protons is assumed to be 1.78 Angstrom, and the calibration parameters are determined my a least squares fit. The automatic calibration will fail if less than 5 geminal proton peaks are found.



A.Widmer, NIBR/CPC/CSG-SB