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


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