About Atom Names and Indexes in WebCocon

Atom Indexes

The atom index is the number in the first column of each line. Originally this was the line number in the inputfile, excluding comment lines. Using this number simplifies the interpretation of the input, but makes the manual creation of the inputfile more difficult. Internally the system continues to use only atom indexes.

Atom Names

In order to facilitate the input of data, WebCocon now accepts Atom names in the form of numbers followed by a single character. The name for an atom is defined in the column "name". WebCocon allows you to switch between the use of names and indexes, and it will try to translate all correlation and NOE data accordingly. Should a name be missing, the switch should be refused with an error message. Using atom names in correlations that are not assigned to an index, or changing atom names while in name-mode normally will break the back translation to indexes.

Switching from Indexes to Names and back

WebCocon always start with indexes. Switching to names and back will trigger a translation of all correlation and NOE data. Should missing information be identified, a switch will not happen. For example, a missing atom name will prevent switching from indexes to names. On the other side, if a name in the correlation table is not found in the name column, ea because a name was changed there, but not in the correlations, switching back to indexes will be blocked.

In general, switching between modes should be done considered buggy end be done very carefully.