Daylight Worksheet - TDT retrieval and editing with xvthor -- with HINTS!

xvthor is an X-Windows client which provides an interface to Daylight Databases through a thorserver connection. To use xvthor, the thorserver must be running and the $DY_THORDB environment variable must be pointed to Daylight Databases. Administration and user configuration will be covered in Day 2, for now this exercise is to provide familarity with the program.

• Start xvthor and open a database
  1. Type xvthor(Sun system) or xvthor4d(SGI system) to start the thor client . With the left mouse button select File, Show Databases select the medchem98demo database.

• Structure Retrieval-Retrieve the full TDT from the database for Dopamine and the 3D structure.
  1. Select the Grins button. Draw in the structure for Dopamine or type in the SMILES on the SMILES line in the xvthor window.

  2. Select the "Show Full TDT" button.
  3. Select the "Show 3D" and try different options of the trackball widget.

• Retrieve TDTs from the database by different identifiers, e.g. try Name= "caffeine", etc.

• Depict the structures in the ~mug/data/SAMPLE.medchem.smi using the Depictions menu.

  1. Select a structure in the list to lookup associated information.

  2. Modify the display using the Props option in the TDT Widget.

• Update a TDT in a Daylight Database
  1. Open another demo database in write mode.

  2. Lookup a structure in the database

  3. Use the Edit menu to add or modify data in the TDT

  4. update the database