next up previous contents index
Next: Stereochemical parameters and molecular Up: Miscellaneous rules and features Previous: File types   Contents   Index

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



next up previous contents index
Next: Stereochemical parameters and molecular Up: Miscellaneous rules and features Previous: File types   Contents   Index
Ben Webb 2004-10-04