FieldView is essentially a 3D molecular viewer capable of generating Cresset’s electrostatic and shape fields for standard molecule files (eg SDF, mol2 etc). The program is extremely flexible, allowing molecules to be entered manually, from 2D files, molecular drawings or created using our internal molecule editor, and once loaded into the program, any data in the original file(s) can be viewed and sorted in a standard table format. FieldView 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 FieldView, the following steps should help you get started with viewing your molecules. See Part 2 of the Guide here.
- Install and double click the Fieldview icon to open an empty file.
- To get started simply load molecules using the ‘Add Molecule’ icon in the menu or click ‘File: Add Molecule’ 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 (eg .using copy paste from Chemdraw or Accelrys Discovery Studio)
- If you try moving the mouse onto the 3d window (Right hand screen), 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 (Left hand screen) by left clicking and dragging from the divider or by using the bottom scrolling slider to view molecule data. Right clicking allows some edit functionality in this data (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. Fieldpoints (4-types) can be toggled on and off independently.
- To view electrostatic surfaces, first change the number in the top menu bar to 3.0, and then click the icons to toggle surfaces – reducing the number increases the size of the field surface . Ensure you toggle the surface view before changing this number. 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 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 visualise 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, use the right hand panel, 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, remove a ligand (save as a mol2 file) from a PDB file (Discovery Studio / Pymol) and save the empty protein as a mol2 file. Use the ‘Add Molecule’ icon to add the empty protein file, left click a protein atom in the 3D panel and assign as protein from the dropdown. You can then use the protein button (Right hand panel) to toggle on/off. The protein will appear in the top dropdown menu as a selectable object. Load the ligand as above and visualize fields in the context of the protein.
- You can Export compounds as sdf, mol file etc using ‘File: Export’, or save the session as a Fieldview file (.fvp) using ‘File: Save Project’.
Still have questions about FieldView? Contact us at firstname.lastname@example.org, and we’ll be happy to help. Click here to view Part 2 of this guide, in which we give you tips for using the Molecular Editor.