3D Structure Editor
Rowan's 3D editor can be used to draw, edit, and optimize molecules. The editor is embedded into Rowan's submit pages and can also be accessed externally at labs.rowansci.com/editor.
To edit a structure you've input, click the pencil icon in the top right corner of the molecule viewer.
To adjust your view, see the instructions in the 3D molecule viewer tutorial.
Selecting Atoms
To select or deselect an atom, click on it. Selected atoms are shown with a transparent green highlight.
Rectangle Select
The "rect. select" tool provides a rectanglular selection of atoms.
If you hold "shift" when you release your click, the atoms within the rectangle will be added to your current selection. (Otherwise, they will replace your current selection.)
Lasso Select
The "lasso select" tool provides freeform selection of atoms.
If you hold "shift" when you release your click, the lassoed atoms will be added to your current selection. (Otherwise, they will replace your current selection.)
Clearing Selection
To clear your selection, you can either (1) double click the canvas or (2) with the default, rectangle, or lasso select tool active, click "Clear selection."
Moving Atoms
To move atoms, use the "Move selected" tool (shortcut: hold "shift" while moving your mouse).
If you click on a selected atom and drag it, you will move it (and your entire selection) in the plane of your screen. With this tool active, you can still click and drag or use the arrow keys to rotate the viewer.
Rotate Selected
To rotate atoms, use the "Rotate selected tool" (shortcut: hold "R" while moving your mouse).
If you click and drag, this will rotate the entire selection around its center. With this tool active, you can still use the arrow keys to rotate the viewer.
Editing Bonds, Angles, & Dihedrals
To edit a bond, angle, or dihedral, use the "Edit bond, angle, or dihedral" tool.
Select two, three, or four atoms (paying attention to their order!) and then input a new value or drag the slider to adjust the value. You can select "Move connected?" to move all atoms associated with the atoms in the coordinate.
Reindexing Atoms
To reindex atoms, use the "Reindex Atoms" tool.
Here, you can change the indices of any of the atoms in your molecule, provided there are no duplicates.
Invert Stereocenter
To invert the stereochemistry at a tetrahedral center, use the "Invert stereocenter" tool.
This will convert the stereocenter between R and S, swapping groups on the stereocenter.
Mirror Structure
To mirror a structure, use the "Mirror structure" tool.
This will mirror the structure horizontally, inverting all stereocenters.
Periodic Table
To add or edit an element, use the "Periodic table" tool.
Select an atom in the periodic table, choose the desired atom geometry (e.g. tetrahedral, linear, square planar). Then click on an existing atom to replace it with the chosen atom & geometry or place the atom in space. The edited/added atom will include enough atoms to achieve the specified valence.
Drawing Bonds
To draw a bond connecting two disconnected atoms, use the "Draw bond" tool.
With the tool selected, click on one atom and drag onto the other. This will connect the two atoms and update hydrogens as needed.
The bonds created using this tool are passed onto the "Optimize with forcefield" tool, which maintains bonding. The "Optimize with GFN-FF" tool and all geometry-optimization workflows do not necessarily respect the bonds created using this tool.
Adding Fragments
To add a fragment from Rowan's fragment library or any arbitrary fragment to the structure you're working on, use the "Add fragment" tool.
You can choose a fragment you want to add from Rowan's fragment library, or input an arbitrary fragment by typing in the molecule's name (sourced from PubChem) or by typing its SMILES sequence. Once a fragment has been selected, it will display in a small 3D viewer in the toolbar column of the viewer.
You can select an atom on the fragment to add at. Click the main structure to add the fragment. If you're not satisfied with how the fragment adds, you can always use the "Undo" button and try again.
Adding Fused Rings
To add a fused ring, use the "Add fused ring" tool.
You can choose a fragment you want to add from Rowan's ring library, or input an arbitrary ring by typing in the molecule's name (sourced from PubChem) or by typing its SMILES sequence. Once a fragment has been selected, it will display in a small 3D viewer in the toolbar column of the viewer.
You can select a bond on the fragment to add at. Click a bond on the main structure to add the fragment. If you're not satisfied with how the fragment adds, you can always use the "Undo" button and try again.
Adding and Removing Hydrogens
To add or remove hydrogens from an atom, use the "Add hydrogens" or "Remove hydrogens" tool and click the atom.
The hydrogens will rearrange to cycle through the basic atom geometries: no bonding, single bond, linear, trigonal planar, tetrahedral, trigonal bipyramidal, octahedral, pentagonal bipyramidal, square antiprismatic, tricapped trigonal prismatic. At this point, geometries beyond 9 bonds aren't supported.
Edit Cell and Periodicity
To create a cell, use the "Edit cell and periodicity" tool, and click "Add cell."
Once a periodic cell has been created, you can edit the lattice vectors using the input boxes and determine whether each is periodic using the checkboxes.
To center your structure in the defined periodic cell, click the "Center system in cell" button. Likewise, to wrap your structure into the defined periodic cell, click the "Wrap system into cell" button.
To create a supercell, use the input boxes to indicate the dimensions of the desired supercell, and click "Create supercell" to add it.
To delete the cell, click the "Remove cell" button.
Solvate Cell
To solvate your defined periodic cell with an explicit solvent, click the "Solvate cell" button.
You can switch between specifying the number of molecules of solvent or its percent composition by clicking the "Specify number of molecules / specify percents" button. You can add a solvent by clicking "Add solvent," then select your solvent from the dropdown, in addition to its composition by using the number input boxes. You can add multiple solvents by pressing "add Solvent" for each one.
Once your solvent is all set up, click "Solvate" to add your solvent to the cell.
Optimizing Dihedrals
To quickly fix clashes, click "Optimize all dihedrals."
You can also fix clashes from a subset of dihedrals with the "Optimize selected dihedrals" tool in the default panel.
Symmetrizing
To symmetrize a molecule, use the "Symmetrize" tool.
The symmetrize tool will detect symmetry, and snap the molecule to symmetry if its geometry is nearly symmetrical.
Optimizing With Forcefield (Subscriber Only)
To optimize the structure you have drawn with a forcefield, select "Optimize with forcefield" (you must be logged in and subscribed to access this feature).
This will use the MMFF94s forcefield to run a quick optimization.
You can select a subset of atoms, and it will only optimize these atoms. The forcefield will attempt to respect any drawn bonds.
Optimizing With GFN-FF (Subscriber Only)
To optimize the structure you have drawn with GFN-FF, select "Optimize with forcefield" (you must be logged in and subscribed to access this feature).
GFN-FF is a general purpose forcefield, and can be used for the first 86 atoms (i.e. up to radon) and charged & open-shell species.
You can select a subset of atoms, and it will only optimize these atoms.
Undo / Redo
To undo or redo changes, use the "Undo" and "Redo" buttons.
Changing Charge or Multiplicity
To change the charge or multiplicity of your system, input the appropriate charge or multiplicity in the number boxes.
Auto-Assigning Bonds
To check that the structure you've drawn is roughly correct or to save yourself time adding or removing bonds, click "Auto-assign bonds."
Adding and Removing Bonds
To add or remove individual bonds, select the default, rectangle, or lasso select tool, select two atoms, and click "Add / remove bond."
Deleting Atoms
To delete atoms, select the default, rectangle, or lasso select tool, select atoms, and click "Delete selected atoms."