Daylight Worksheet - Rubicon

Rubicon, "Rule-Based Invention of Conformations", generates 3D coordinates for a TDT file using a simple set of rules, or rules generated from a training set with autorules.

1. Generate 3D coordinates to the day1.tdt dataset created in the PCModels exercise or use the ~mug/data/day1.tdt file.
   • List Rubicon options
     • rubicon -options
   • List current settings
     • rubicon -settings
   • Generate 3D coordinates with standard ruleset
     rubicon < day1.tdt > day1.3d.tdt
2. Generate 3D coordinates using rules generated from a training set and autorules. Obtain the training set from a substructural search of the medchem98demo database and thorlookup to obtain the $D3D data.
   • Open the medchem98demo database in merlin and search for a substructure from the ~mug/data/day1.tdt dataset.
   • Save the search results in a tdt file
   • Use thorlookup to find the $D3D data
   • generate a rule set
     • autorules < hitlist.tdt > output.rules
   • Generate 3D structures for day1.tdt dataset using the new ruleset