##
File types

MODELLER uses a number of standard filename extensions to indicate the type of data stored in a file (Table 5.1). The extensions are generally not mandatory, only very helpful.

Table 5.1: List of file types.

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 or USER format
`.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