GUI Features: con't
     
  Set Torsions Trident contains a flexible procedure for conformational analysis with refined default settings for conformational searching and also provides tools for users to customize selection of torsion angles and atoms as well as defining rotation and ring puckering variables.
     
  Alignment &
Similarity
Molecules may be aligned to a "parent" molecule using atoms, CFD's, or pharmacophores as alignment centers. Similarity analysis is available on molecules or conformer libraries using atoms, CFD's or pharmacophores as the basis for similarity searching.
     
  Extract Ligands Small molecules bound to biopolymers are automatically detected and identified for Protein Databank (PDB) files. Bound ligands can be "extracted" for further analysis including structure and property calculations, conformational searching, and similarity analysis. Ligands can be optionally retrieved with environmental structures, chemical function descriptors, excluded volume centers, or with the protein/nucleic acid structure. Additional filters allow for "repair" of bonding and "growing" hydrogens.
     
  Tautomers Trident automatically detects proton isomers of heteroatoms (N,O,P,and S) and optionally generates a list file with all tautomer structures.
     
  Dialogues:  
     
  Calculations A single dialogue specifies all computational tasks, structure/properties calculations, graphics requests, molecular shape calculations, and similarity analysis.
     
  Graphics An easy to use dialogue for selecting display of calculated graphical surfaces.
     
  Properties Property dialogues are available for all objects in Trident and provide additional useful information on molecules, atoms, bonds, graphics, biopolymer residues, ligands, CDFs, substituents, and plots.
     
  Databases A search database dialogue is available, allowing the user to specify details of the query as well as database is to be searched.
     
  Spreadsheet A spreadsheet is available to collect and analyze calculated quantities on lists of molecules. Convenient tools for totals, averages, Boltzmann averages, and linear regression analysis are available. Spreadsheet data may also be copied to Microsoft® Excel® and other productivity tools.