| Extension |
Description |
| .top |
TOP script with instructions for a MODELLER job |
| .log |
log output produced by a MODELLER run |
| .ali |
alignment or sequences in the PIR format |
| .pap |
alignment or sequences in the PAP format |
| .aln |
alignment or sequences in the QUANTA format |
| .aln |
alignment or sequences in the INSIGHTII format |
| .seq, .chn |
sequence(s) in the PIR alignment format |
| .cod |
list of sequence codes |
| .grp |
list of families in PDB |
| .atm, .pdb, .ent |
atom coordinates in the PDB or GRASP format |
| .crd |
atom coordinates in the CHARMM format |
| _fit.pdb |
fitted protein structures in the PDB format |
| .ini |
initial MODELLER model |
| .B* |
MODELLER model in the PDB format |
| .D* |
the progress of optimization |
| .BL* |
MODELLER model in the PDB format, in loop modeling |
| .DL* |
the progress of optimization, in loop modeling |
| .IL* |
initial MODELLER model, in loop modeling |
| .V* |
violations profile |
| .E* |
energy profile |
| .rsr |
restraints in MODELLER format |
| .lrsr |
restraints in MODELLER format, in loop modeling |
| .sch |
schedule file for the variable target function optimization |
| .mat |
matrix of pairwise protein distances from an alignment |
| .mat |
matrix of pairwise residue type-residue type distance scores |
| .sim.mat |
matrix of pairwise residue type-residue type similarity scores |
| .lib |
various MODELLER libraries |
| .psa |
residue solvent accessibilities |
| .sol |
atomic solvent accessibilities |
| .ngh |
residue neighbors |
| .dih |
mainchain and sidechain dihedral angles |
| .ssm |
secondary structure assignment |
| .var |
sequence variability profile from multiple alignment |
| .asgl |
data for plotting by ASGL |
