The structure fragment database (DGLOOP)
Introduction.
Implications of the algorithm
Searching in the database
Finding stretches (DGFIND)
Inserting residue(s) using the database (DGINS)
Finding alternative conformations (DGFIX)
Mutating using the database (DGMUT)
Contact searches (DGCONT)
Replacing a residue with a hit (DGREP)
Display fragments
Movie of fragments (DGGRA)
Showing all fragments at once (DGGRAL)
Listing hits (DGSHOW)
Working with alpha carbons only
Builing a structure from alpha carbons (CATOAL)
Keeping only alpha carbons (ALTOCA)
Rotamer searches
Single rotamer searches (DGR1-1)
Single rotamer searches (DGROTA)
Multiple residue rotamers at one position (DGRN-1)
One residue type rotamer for a range of residues (DGR1-N)
All rotamers for a residue range (DGRN-N)
Self rotamers (DGRSLF)
geometric best rotamers for a residue range (DGRS-N)
Fragment group administration
Resetting the group length (SETLEN)
Initializing the groups (INIGRP)
Showing the search groups (SHOGRP)
Database related parameters
Parameters (PARAMS)
Tightening the parameters (TIGHT)
Relaxing the parameters (RELAX)
Resetting the default parameters (RESPAR)
Showing dgloop parameters (SHOPAR)
Automatic mutant prediction (DGDMUT)
Statistics on groups of hits