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Import

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PURPOSE OF PROGRAM:  Converts a PIPP peak table (.PCK file) into an intermediary
database format. The intermediary database file can in turn be converted into 
an X-PLOR NOE distance-restraint file using the companion program, "makexplor".

USAGE:  import in_file out_file [2D|3D|4D]

COMMAND LINE ARGUEMENTS:

import:   the name of the program
in_file:  a PIPP .PCK file
out_file:  output file name
[2D|3D|4D]: optional flag designating the dimensionality of the experiment
            analyzed in PIPP (Default = 3D)

EXAMPLE:

The following example is for "importing" data from a .PCK derived from
analysis of a 3D 13C-edited NOESY spectrum:

import noe_13c_3d.PCK noe_13c_3d.dbase 3D

FILE FORMATS:

Input file must be a valid, unmodified, PIPP .PCK file.  Upon execution, 
the program, will prompt the user for an experiment name (10 characters 
maximum) and date (10 characters maximum) that will be added to output 
database (see below).

The output file has the following kind of format:

.
.
9        0    noesy15n    08/08/00
W 65   HA    : W 65   HN      0 - 0 [ 2 ]
5.56        9.91  104.79
0.1750    0.4730   4.9086  0.3700
0.00      0

10       0    noesy15n    08/08/00
W 65   HE1   : I 72   HG2#    0 - 3 [ 1 ]
0.44        9.93  131.16
1.5500    7.1300   4.9086  0.2174
0.00      0
.
.

For each entry in the database text file that is created, there are five lines which
contain the following pieces of information:

Line1:
o Restraint ID
o A blank field that is used by the program internally (typically set to zero in the output)
o The experiment name supplied by the user upon execution
o The experiment date supplied by the user upon execution

Line2:
o The residue number for proton 1
o The atom name for proton 1
o The residue number for proton 2
o The atom name for proton 2
o The "class" to which proton 1 belongs �The "class" to which proton 2 belongs
o [1] or [2] indicating as to whether the diagonal proton is proton1 or proton 2

Atom Classes are defined as follows: amide (0), single aliphatic proton (1),
prochiral or degenerate methylene proton (2), and methyl proton (3)

Line3:

o chemical shift values of the NOE peak position:  F3, F2, F1

Line 4:

o experimental NOE peak intensity x 10^-6
o experimental diagonal peak intensity (if available, otherwise average value for class) x 10^-6
o average diagonal peak intensity corresponding to the relevant class of diagonal protons
o ratio of the NOE peak intensity to diagonal peak intensity (experimental if available)

Line 5:

o blank field to hold distance estimate (not calculated by this program, set to 0.00)
o A blank field that is used by the program internally (typically set to zero in the output)

BUGS:

The program becomes unstable if the dimensionality of the .PCK
file does not match that what you specified.  This is the MOST
common reason for the program crashing. 

Another bug is the fact that the source and destination protons
may not be properly identified when a 4D NOE data set is analyzed.  
The reason for this is that the program was initially written 
for handling 3D data, and the appropriate code for handling all
aspects of a 4D has not yet been added.

Along the same lines, when a 4D .PCK file is converted, the 
chemical shifts for all 4 nuclei are not reported (the last
carbon atom is omitted).  Likewise, when a 2D .PCK file is 
converted, the "Y" and "Z" chemical shifts are set to be the
same.  

Other bugs:  email hinck@uthscsa.edu
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Last updated on July 17, 2003