This routine wraps the script detect_sugars, which detects cyclic (5- or 6-member ring) saccharide residues in PDB files. Use of this routine will result in user-friendly output. The detailed, unfriendly, output from detect_sugars (see ‘See Also’, below) can be preserved if that is desired.
PDBSugarID PDB_file.pdb Outfile [keep] [details_file_name]
PDB_file.pdb is a properly formatted PDB file possibly containing carbohydrate residues.
Outfile is your preferred output file name.
keep is the literal word ‘keep’. It is optional. If specified, the raw, verbose output from detect_sugars will be saved. By default, it is not saved.
If keep is used, but details_file_name is not set, the filename is:
… where Outfile is replaced with the filename you specified on the command line.
details_file_name is the name of the file into which you want the details to be saved.
GEMSHOME must be set.
The script GEMSHOME/bin/detect_sugars must exist and be usable.