| env = <environ> | MODELLER environment | |
| alnfile = <str:1> | file containing template-sequence alignment | |
| knowns = <str:0> | template codes in alignment | |
| sequence = <str:1> | sequence code in alignment | |
| deviation = <float:1> | control amount of randomization | |
| library_schedule = <int:1> | optimization schedule | |
| parlib = <str:1> | parameter library to use | |
| csrfile = <str:1> | user-provided restraints file | |
| inifile = <str:1> | user-provided initial model file | |
| assess_methods = function(s) | assessment functions |
See section 2.2.3 for an example.