3D Structure Editor
To use Rowan's 3D structure editor, you can go to labs.rowansci.com/editor.
The editor is also embedded into Rowan's submit pages. To edit a structure you've input, click the pencil icon in the top right corner of the molecule viewer.
Selecting Atoms
To select or unselect an atom, click on it. Selected atoms are shown with a transparent green highlight.
Rectangle Select
The "rectangle select" tool lets you click and drag a rectangle to select 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 lets you click and drag to lasso 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.
With this tool, you can click and drag to rotate the viewer. You can also rotate the viewer with arrow keys.
You can click atoms to select them.
If you click on a selected atom and drag it, you will move it (and your entire selection) in the plane of your screen.
Editing Bonds, Angles, & Dihedrals
To edit a bond, angle, or dihedral, use the "Edit bond / angle / dihedral" tool.
Select two, three, or four atoms (paying attention to their order!) and then input a new value for the selected measure.
Replacing Atoms / Periodic Table
To select any element from the periodic table, use the "Replace atom" tool.
Select an atom, choose the desired atom geometry, and click on an existing hydrogen or other atom to replace it with the chosen atom & geometry.
Adding Fragments from the Fragment Library
To add a fragment from Rowan's fragment library to the structure you're working on, use the "Add fragment" tool.
You can choose the fragment you want to add from the library, and 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 satisified 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.
Undo / Redo
To undo or redo changes, use the "Undo" and "Redo" buttons.
Optimizing Dihedrals
To quickly fix clashes, click "Optimize dihedrals."
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 atoms, 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."