[ New Chemical | Smiles | Load | Extract | Convert | Properties | Edit Sketch | Edit Ligand | Tautomers | Stereoisomers | Save SDF | Cluster | Chemical Browse ]

A quick start guide on how to work with small molecules and ICM Molecular Tables.

2.4.1 How to Make a New Chemical

Draw new compounds by using the ICM Molecular Editor.

The molecular editor can be activated by:

• Clicking on the Open ICM Molecular Editor button shown below.

OR

• Select Chemistry/Molecular Editor and the editor as shown below will be displayed.

2.4.2 How to Use a SMILES String to Generate a Molecule

If you have a single SMILES string you can:

• Open the ICM Molecular Editor
• Select Edit in the ICM Molecular Editor
• Select Add Smiles and enter the string.

or...

If you have a ".smi" file (usually smiles and then some space separated extra data in each line) you can:

• File/Open" and then select "Smiles format (*.smi)" in the open file dialog.

or...

If you have a comma (or tab) separated file where one column contains smiles. In this case you need to

• Read it into ICM as normal spreadsheet table. File/Open
• Chemistry/Convert Smiles to 2D".

2.4.3 How to Load a Small Molecules into ICM

To load a small molecule into ICM:

• File/Open
• Small molecule files generally have the file type .mol, .mol2 or sdf
• Depending on the file type the chemical will either be loaded into an ICM Molecular Table or in the ICM Workspace.

2.4.4 How to Extract a Ligand from a PDB file into an ICM Molecular Table

• As an example we will use the PDB structure 1STP. Type 1STP in the pdb search tab and press return.
• Right click on the ligand (btn) in the ICM Workspace and select "Extract Ligand"
• You can choose whether to keep the 3D coordinates or just 2D
• The ligand is then extracted into an ICM Molecular Table.

2.4.5 How to Convert a Chemical in an ICM Molecular Table into 3D

To do this:

• Select the chemical or chemicals in the ICM Molecular Table you wish to convert to 3D. You can do this by clicking on the row number whilst keeping the CTRL key pressed down.
• Right click on the chemical table and select Chemistry/Convert 3D and Optimize
• The converted chemical will then become an object in the ICM Workspace.

2.4.6 How to Add Properties to a Molecular Table

To read a chemical table into ICM:

• File/Open and look for sdf files.

To add a chemical property to the table.

• Right click on the 'mol' column header and select Insert Column...

• Click on the drop down 'Function' button and select chemical.
• Select which property you wouls like to add and click OK.
• The property you selected will be displayed in the table.

2.4.7 How to Edit a Molecule in an ICM Molecular Table

To edit a molecule in an ICM molecular table:

• Right click on the chemical sketch in the ICM Molecular Table.
• Select Edit Molecule ....
• The ICM Molecular Editor will be displayed.
• Edit the molecule and then select File/Save and Quit inside the ICM Molecular Editor window. Changes will then be added to the sketch in the table.

2.4.8 How to Edit a Ligand in a 3D structure.

To edit a ligand in a 3D structure:

• As an example we will use the PDB structure 1STP. Type 1STP in the pdb search tab and press return.
• Right click on the ligand (btn) in the ICM Workspace and select "Edit/Edit Compound"
• The ICM Molecular Editor will be displayed.
• Edit the molecule and then select File/Save and Quit inside the ICM Molecular Editor window.

2.4.9 How to Generate Tautomers

To generate the tautomeric structures of a chemical in an ICM Molecular Table.

• Right click on the chemical sketch in the ICM Molecular Table. More than one compound can be selected (see section on Table Selections).
• Select Chemistry/Enumerate Tautomers
• A new table will be generated.

2.4.10 How to Generate Stereoisomers

To generate the stereoisomers of a chemical in an ICM Molecular Table.

• Right click on the chemical sketch in the ICM Molecular Table. More than one compound can be selected (see section on Table Selections).
• Select Chemistry/Enumerate Stereoisomers
• A new table will be generated.

2.4.11 How to Save an ICM Molecular Table as an SDF File

To save an ICM Molecular Table as an SDF file

• Right click on the table header and select "Save As.."

2.4.12 How to Cluster a Set of Chemicals

To cluster a set of compounds in a an ICM Molecular Table:

• Select the rows of the table you wish to cluster. If you wish to cluster all the chemicals in the table there is no need to make any selection.
• Right click and select Clustering...

NOTE: More information regarding clustering can be found in the Tables section of the GUI manual.

2.4.13 How to Browse in 3D

If you have an ICM molecular table (Chemical Spreadsheet) displayed you can browse the compounds in the graphical display by right clicking on the "mol" column header and select Set 3D Browse Mode.

See: Set Chemical Table 3D Browse Mode