Objective

To read and display chemical structures.

Background

Small molecules are generally stored in three different file types - SDF, MOL/MOL2 and SMILES. An SDF file is a database of chemical structures. When chemical structure(s) are loaded into ICM they are automatically displayed in a chemical table. In this lesson we will read a SDF file that contains compounds extracted from the PDB.

Instructions

1. File/Open locate the file called ricinLigands2D.sdf - this file is provided in the ICM distribution. You should be able to locate it in $ICMHOME or C:/Program Files/MolSoft OR use any other SDF file as an example.
2. The compounds will be displayed in a table called ricinLigands2D.
3. To arrange the compounds in a grid as shown below. Right click on the table and a menu will be displayed select Table View/Grid View.