Skip to main content
Center for Biomolecular NMR Spectroscopy
HomeUser GuidelinesSpectrometersSchedulingFeesUNIX Software InformationEducation and USER BASELinksContact Us
Cols2Pipp

Bar Break


PURPOSE OF THE PROGRAM:  Converts columnar-style chemical shift table into a PIPP
shift table.

USAGE:    cols2Pipp <in_file> <out_file> [atom_substitution_table]

cols2Pipp:    Program Name
<in_file>:    Name of Shift Table Input File
<out_file>:   Name of the PIPP Shift Table Output File
[atom_substitution_table]:      OPTIONAL ARGUEMENT which specifies the
                                atom_subsitution_table that determines
                                how atom names will be mapped to the
                                column headers; Default file is:
                                /u/people/ahinck/bin/atom_sub_tbl

FILE FORMATS:

Input File:    Must contain column type data in text format delimited by
one or more spaces.  The number of columns should equal the number of unique
atom types + 2. Column 1 should contain the residue number.  Column 2
should contain the residue type using the one-letter amino acid code in CAPS.
The number of rows should equal the number of residues + 1.  Row 1 should
contain the atom designators.  It is suggested that these be set to those which are
identical to those used by PIPP, although this is not entirely necessary since the
program also includes a facility for mapping atom names (see below).  Since not all
amino acids will have chemical shift entries corresponding to each of the column
headers, you will need to insert dummy entries to maintain correspondence between
individual chemical shift values and the column headers.  In its present
implementation, the program assumes that blank entries will include the
character 0.

Output File:    The output format will be in the PIPP format provided that the
amino acid codes are properly designated in column 1 and the atom designators
used in the first row (in conjunction with any atom name mapping that has been
defined in the atom substitution file) are consistent with the nomenclature used
by PIPP.

OPTIONAL Atom Substitution Table:  This program features an atom name mapping facility
which works as follows.  Chemical shift entries in specific columns for specific amino
types can be designated an atom name that is different from that designated in the
column header in the input file by defining how you would like the atom names mapped.
This mapping is accomplished using an atom substitution table, which is a separate
text file that is read in by the program.   The default file to be used for this
 purpose is /u/people/ahinck/bin/atom_sub_tbl, although the user can create and
specify his or her own atom substitution table.  The format of atom substitution
file is as follows:  It contains three columns which correspond
to the amino acid type specified by three letter codes (column 1) and how the atom
name as specified in the column header of the input file (column 2) should be
designated in the output PIPP shift table (column 3).

LIMITATIONS:

Line lengths in the input file are limited to 755 characters.
Data size is limited to 75 columns (73 atoms) by 399 lines (residues).
Character strings for atom designators or shift values are limited to 10.
Characters.

ERRORS:

Errors are reported to standard output and can be redirected to a file
using the ">" idiom.
Bar Break

Home  -  Getting Started  -  Spectrometers  -  Scheduling  -  Fees  -  UNIX Information  -  Technical Resources  -  Links  -  Contact
UTHSCSA  -  Center for Biomolecular Structure Analysis  -  Department of Biochemistry  -  Disclaimer  -  Copyright

Last updated on July 17, 2003