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PURPOSE OF PROGRAM:  To convert a intermediary NOE restraint database file
(from the companion program "import") into an X-PLOR NOE distance restraint file.

USAGE: makexplor dbase_input xplor_output ref_dist ref_int noepow [-ps_sub or -ps_sub2] [-no_intra]

COMMAND LINE ARGUEMENTS:

makexplor:               program name
dbase_input:             input database filename
xplor_output:            output X-PLOR distance restraint file
ref_dist:                a reference distance to be used for calibration of interatomic distances
ref_int:                 a reference NOE peak intensity to be used for calibration of
                         interatomic distances
noepow:                  the coefficient to be used in the isolated spin pair approximation
                         for calculation of interatomic distances (widely assumed to be 6,
                         but in practice typically somewhat less)
-ps_sub or -ps_sub2:     an optional argument specifying that pseudoatom substitution be applied
-no_intra:               an optional argument specifying that intraresidue restraints be
                         excluded from the output file

FILE FORMATS:

Input File:  NOE distance restraints in the "database" format created by the C-program import (a des
cription of this format can be found in the help files for the program import)

Output File:  X-PLOR distance restraint file (validity of the atom selections, however, are not
verified and will thus be dependent upon their correct designation in the PIPP shift table, in
conjunction with any modifications that occurred using pseudoatom substitution)

DESCRIPTION OF PARAMETERS:

ref_dist, ref_int, and noepow - these parameters determine how NOE peak intensities are
converted into NOE distance restraints using the isolated spin-pair approximation (ISPA) as
follows:

exp_dist = ref_dist(ref_int/exp_int)^noepow

where ref_dist is a reference distance between two protons that are separated by a fixed covalent
distance (such as the Hd - He protons in an aromatic ring) and ref_int is the corresponding
observed normalized NOE intensity (defined as the NOE peak intensity divided by the diagonal
peak intensity) that is observed between these two protons.  On the basis of either the theoretical
value for noepow (noepow = 6), or an empirically determined best suited value for noepow
(typically found to be somewhat less than 6 owing to the effects of spin diffusion; see below), a
distance is calculated for a given observed NOE (exp_dist) based on an observed normalized
NOE peak intensity (exp_int; defined as the NOE peak intensity divided by the diagonal peak
intensity).

-ps_sub or -ps_sub2:  these command line options determine whether or not the user applies
pseudoatom substitutions in creating the X-PLOR NOE distance restraint output file.  This may
be necessary in some cases since it is possible to include in a PIPP shift table atom names which
are NOT considered valid atom names by the program X-PLOR.  An example of this are atom
designators such as HB1|HB2 or HB2|HB1 in a PIPP shift table (these are potentially desirable
as atom designators in PIPP shift table since it may be possible to stereospecifically assign these
protons).  By default the program reads the file /u/people/ahinck/bin/not_stereo which in turn
determinations which atom pseudoatom substitutions will be made (the atom type to be
substituted in the first column, pseudoatom to be substituted in the second column).  The user has
the option of defining their own pseudoatom substitution file by using the command line option
-ps_sub2 (in place of the normal option -ps_sub).  In this case, the pseudoatom substitution file
is assumed to have the name not_stereo and to reside in the same directory in which the program
was executed.

-no_intra:  this command line option causes the program to exclude any intraresidue NOE
distance restraints in the X-PLOR output file

WARNINGS PRODUCED DURING PROGRAM EXECUTION:

Upon conversion of normalized NOE peak intensities into NOE distance restraints,
the program checks to determine whether the calculated distances
fall between a reasonable lower (covalent radii) and upper bound (ca. 5 angstroms after having
applied any pseudoatom corrections).  The number of restraints which are observed to exceed
either the lower or upper bounds can be followed as a function of the values used in the
distance calibration, as well as the value for noepow.
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Last updated on July 17, 2003