TorchLite is a powerful 3D molecular viewer capable of generating Cresset’s electrostatic and shape fields for standard molecule files (e.g.: .sdf, .mol2, etc.). The program is extremely flexible, allowing molecules to be entered manually, from smiles strings, 2D files, molecular drawings or created using our internal molecule editor. Once loaded into the program, any data in the original file(s) can be viewed and sorted together with calculated physical properties provided by TorchLite in a molecular spreadsheet. TorchLite has tools to enable download and interrogation of protein ligand complexes and has a simple minimization tool allowing the visualization of reasonable conformations derived from the original 2D input. Additionally, various 3D field displays are available with molecules editable showing ‘on-the-fly’ changes in the field visualizations.
Once you’ve downloaded TorchLite, the following steps should help you get started with viewing your molecules.
See Part 2 of the Guide here.
- Install and double click the TorchLite icon to open an empty file.
- To get started simply load molecules using the ‘Open’ button and browse to add an appropriate file (.sdf, .sd, .mol, .mol2 etc), which will then appear in both 2D and 3D format. Alternatively, click ‘Edit: Paste’ to paste molecules from clipboard (e.g: using copy paste from Chemdraw or Accelrys Discovery Studio).
- If you try moving the mouse onto the 3D window, the bottom left panel tells you which mouse clicks will move the molecule in the 3D viewer.
- You can scroll through the 2D molecule window pane by left clicking or by using the green arrows below the 3D window. Right clicking on molecules in the table gives a context menu that operates on the molecule that was clicked (eg. copy, rename etc).
- Molecules can be selected by left clicking on the 2D panel. In the menu: “selected molecules” indicates that display options apply to the currently selected molecule. Display settings can be toggled by clicking icons in the top menu bar. Display settings can also be toggled to apply to all molecules using this dropdown option. Field points (4-types) can be toggled on and off independently.
- To view electrostatic surfaces, click the +ve or -ve icons to toggle surfaces – reducing the number increases the size of the field surface. Yellow surface fields usually require a smaller number (2.00) relative to the electrostatics (3.00-4.00) for a good view.
- To make multiple selections, hold shift or Ctrl before selecting from the 2D panel – this is particularly good if you make a copy of a compound and apply different visualizations to each – and visualize by toggling the grid icon (Right hand) panel. Hover the mouse over this panel to display the icon name.
- Hitting the ‘Delete’ key will delete all the selected molecules.
- To filter the molecule table, use the filters window (enabled with View->Windows), which holds all of the available filters. Choose any data column from the dropdown menu to apply filters using the sliders which appear upon column selection.
- To view protein-ligand complexes, open the .pdb complex using File->Open or download the .pdb file directly by specifying the .pdb code in File->Open PDB. The protein importer will open with the protein displayed in 3D and the chains and residues displayed in a table.
- Sort this table on “Structure” to find the ligand.
- Highlight it by clicking on its structure then click the “Use as Reference” button on the right hand side.
- Optionally choose to delete uninteresting or distal chains by selecting in the table and clicking “Delete”.
- Waters can be deleted with the “Delete waters” button.
- You can Export compounds as .sdf, .mol file etc using “File: Export”, or save the session as a torchV10 file (.fpj) using “File: Save Project”.