check_ppm (V1.1)

Purpose: This program checks the validity of the particular atom names in a PPM shift file. Unrecognized atom names are either corrected or flagged.


Description

Run the program by typing "check_ppm". The user is prompted to enter an input PPM shift file and an output file.

The check_ppm program checks each atom name in the input PPM file. If the name is valid for the corresponding amino acid, the shift is written to the output file. For a name to be valid, it must exist in the $INSTALL_DIR/lib/amino.spec file.

For atom names which are not found, the program will try to "correct" for the name by looking in $INSTALL_DIR/lib/amino.correct . This file contains entries of the other ways atoms can be specified. If the program cannot find the correction entry here, the particular shift is not written to the output file and the error reported.

The check_ppm program maintains a log file in the current working directory called "check_ppm.log". Here is recorded every atom name which has been corrected and those which could not be identified.


Last modified: Mar 21, 1997

Robert Boyko - robert.boyko@ualberta.ca