Input: script file, alignment file, PDB file(s) for template(s).
Output:
job.log | log file |
job.ini | initial conformation for optimization |
job.rsr | restraints file |
job.sch | VTFM schedule file |
job.B9999???? | PDB atom file(s) for the model(s) of the target sequence |
job.V9999???? | violation profiles for the model(s) |
job.D9999???? | progress of optimization |
job.BL9999???? | optional loop model(s) |
job.DL9999???? | progress of optimization for loop model(s) |
job.IL9999???? | initial structures for loop model(s) |
The main MODELLER routines used in each step are given in parentheses.
stereochemical | restraint_type = 'bond angle dihedral improper' |
mainchain dihedrals Φ, Ψ | restraint_type = 'phi-psi_binormal' |
mainchain dihedral ω | restraint_type = 'omega_dihedral' |
sidechain dihedral χ1 | restraint_type = 'chi1_dihedral' |
sidechain dihedral χ2 | restraint_type = 'chi2_dihedral' |
sidechain dihedral χ3 | restraint_type = 'chi3_dihedral' |
sidechain dihedral χ4 | restraint_type = 'chi4_dihedral' |
mainchain CA-CA distance | restraint_type = 'distance' |
mainchain N-O distance | restraint_type = 'distance' |
sidechain-mainchain distance | restraint_type = 'distance' |
sidechain-sidechain distance | restraint_type = 'distance' |
ligand distance restraints | AutoModel.nonstd_restraints() routine |
user defined | AutoModel.special_restraints() routine |
non-bonded pairs distance | restraint_type = 'sphere'; calculated on the fly |