Some errors are recoverable. For those errors, TOP variable MODELLER_STATUS becomes 1. A test is then performed: If MODELLER_STATUS is equal or greater then STOP_ON_ERROR, execution stops; otherwise, the control is passed back to the calling TOP routine where execution continues with the next TOP command. It is then up to your TOP script to deal sensibly with the failure of the preceding command. For example, this flexibility allows derivation of multiple models and searching for many sequences, even if some cases abort due to convergence problems.
There are five kinds of messages that MODELLER writes to the log file, indexed 1 to 5: long output from the MODELLER commands, short notes to do with the execution of the program (files opened, etc.), warnings identified by `_W>', errors identified by `_E>', and the messages about the status of dynamic memory allocation. The five elements in the TOP variable OUTPUT_CONTROL[1:5] can assume values of 0 or `not 0'; 0 indicates that the corresponding information is not written out, `not 0' indicates that it is.2.1Thus, different amounts of output can be selected. If everything is well, OUTPUT_CONTROL = 1 0 0 1 0 is convenient because no execution messages, warnings, and dynamic memory reports are written out; for debugging, use OUTPUT_CONTROL = 1 1 1 1 1. To increase the detail of the dynamic memory status reports, set the last flag to 2.