Format of the command description

For each command, the list of arguments, brief description, and an example are given. Additional background information may be found in Chapter 5. The variable types are described as follows (see also Table 4.1):

<integer:1>	an integer variable or constant
<real:1>	a real variable or constant
<string:1>	a string variable or constant
<logical:1>	a logical variable or constant
<integer:0>	a vector of any length with elements <integer:1>
<integer:N>	a vector of $N$ elements <integer:1>
etc.	the same for real, string, and logical types

Table 2.1: 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