STARch help

STARch converts chemical shift data from several formats to NMR-STAR format.

Input data

Input file(s) must contain at least residue sequence codes (numbers) and residue labels, and the {residue code, residue label} pairs must be unique. If either is missing from input file (or input file contains duplicate labels/codes) STARch will generate an error message and stop.

Supported input formats:

XEASY

PIPP

"Format1" (space-delimited table, one atom per line)

"Format4" (space-delimited table, one residue per line)

"Format2" (each residue occupies one or two lines, field lengths and starting columns are specified at the top of the file)

"NucleicAcid" (a less restrictive variant of Format2 above)

NMR-STAR 2.1

STARch output

By default STARch prints out an NMR-STAR 2.1 loop (table) of chemical shifts; there is an option to print out a comma-separated file instead. If STARch is running in verbose mode (default for web-based version), it will also print out warning messages, if any. If STARch is unable to convert the input, it will print out error message(s); no other output is generated.

Some input files may contain extra values or comments. These are written out as NMR-STAR comments. (NMR-STAR comments start with '#' and continue to the end of the line.) In some cases STARch will output comments in a separate row that contains only residue sequence code, residue label, and the comment.

In addition, STARch prints some of its warnings as NMR-STAR comments. For example, if chemical shift value for the atom is "n/a" STARch will add the comment "shift value = n/a" (the value is supposed to be a floating-point number).

If nomenclature conversons are turned on, STARch will add atom types if they aren't present in input. Atom type defaults to the 1^st character of atom name.

STARch will preserve trailing zeroes in chemical shift value (and error): they are assumed to be significant.

Details of STARch output formats.

Errors and warnings

STARch error/warning messages are printed below the data loop. General format of the message is

[ERR|WARN]:line_number:residue_sequence_code residue_label atom_name message_text

Line numbers, sequence codes, lables and/or atom names may be omitted. Also, since some formats may contain continuation lines or optional extra lines (e.g. field count), line numbers in STARch messages may be off by one or two.

Error messages begin with ERR. They are generated when STARch cannot convert the data, e.g. when input file is in a wrong format. There will be no output other than the error message.

Warning messages begin with WARN. These are generated when STARch encounters a non-critical (i.e. processing can continue) error, or when the input contains an incorrect value.

Last updated: Fri Jan 3 15:23:17 CST 2003