[ Chemical Display | Adding Column | Grid View Multiple Columns | Sort Column | Filter Column | Rename Column ]

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.

2.5.2 How to Add Columns to a Chemical Table

1. Using the ricinLigands2D.sdf file from the previous example (**File/Open locate the file called ricinLigands2D.sdf) we are going to add some columns to the table. If your table is still in grid view please return to row view by right clicking on the table and selecting Table View/Row View.

NOTE You can toggle between grid view and row view by using the keyboard buttons Ctrl + T.

Firstly we are going to add a column with the molecular weight of each chemical.

• Right click on the column header mol as shown below and select Insert Column

• Select the Function button and use the drop down menu to find Chemical/MolWeight - as shown below.

• A column entitled MolWeight will be added to the table.

• Repeat the Insert Column instructions for LogP, LogS and MolPSA and your table should look something like the one shown below.

2.5.3 How to Create a Grid View.

• Using the table we made in the previous example we will display each chemical along with its molecular weight in grid view.
• To do this select the mol and MolWeight column - this can be done by clicking on the column header and hold the Ctrl key on your keyboard.

• 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.

NOTE: Custom grid options (define number of columns) can be found in right click Table View/ Custom option.

2.5.4 How to Sort a Column

• Using the table we made in the previous example we will sort the MW column from low MW to high.
• Right click on the column header MolWeight and select the option Sort

2.5.5 How to filter a table by the values contained within a column.

• Using the table we made in the previous example we will filter the column and only display those compounds which have a molecular weight between 200 and 350.
• Right click on the MolWeight column and select Filter/Custom
• Using the drop down arrow select is greater than or equal to 200 and is less than or equal to 350 as shown below.

• Only 3 compounds will now be displayed. A symbol as shown below indicates the column has been filtered.

• Now we will remove the filter by right clicking on the column header and selecting Filter/Clear

2.5.6 How to Rename a Column and Add Data.

• Using the table we made in the previous example we will rename the column NAME_ and add data to this column.

To rename a column

• Right click on the column NAME_ and select Rename Column... and for this example we will enter the name Binding_Affinity

To add data to the column

• Right click on the column header and select Edit Mode.

• You can now add data to the column by double clicking and typing in data.

Notes and Things to Try:

• Try inserting a row into the table.
• Try different ways of displaying the compounds. Try selecting different columns in the table and displaying based on this. (see section 9.1.3 of the User's guide on how to make table selections)
• Try selecting rows or columns.
• We will learn how to edit structures in the next lesson but if you want to edit a structure you can select the Edit Molecule option and the ICM Molecular Editor will be displayed.
• You can copy and paste molecules into other applications such as word or other molecular drawing software.