The Build panel provides basic selection and drawing tools, and bond calculation / augmentation methods.

Build Panel

Select Group

Select Group

Atoms

Shortcut: Escape

The primary selection mode (and the mode that Aten sits in when simply visualising), this allows individual atoms to be clicked or a selection-box to be drawn around multiple atoms in order to select them. With the Shift key pressed the selection state of the atoms is toggled, and if Ctrl is held down the atoms are removed from the current selection.

Bound

Select individual bound fragments - clicking on any atom in a molecule will select the entire molecule by performing a recursive tree-select from that atom. With the Shift key pressed the selection state of the fragment is toggled, and if Ctrl is held down the fragment is removed from the current selection.

Element

Select all elements of the same type as the clicked atom. Again, holding Shift toggles the selection while holding Ctrl removes them from the selection.

Draw Group

Draw Group

Draw

Sketch individual atoms and bonds with the Draw tool. New atoms are created as the currently-selected Element.

Fragment

Draw molecular fragments, and append molecular fragments to existing atoms. Long-pressing the Fragment button shows the fragment selection popup, from which the available drawing fragments can be browsed and one selected for drawing.

In this mode a copy of the selected fragment is 'attached' to the mouse cursor and can be drawn in any desired position, but will snap to existing atoms that possess an available binding site (according to their current bond involvement). Left-clicking will draw a copy of the fragment in its current position, while left-click-dragging allows the copy to be rotated before it is placed - if snapped to an existing atom, the fragment is rotated about the new bond vector. If the atom under the mouse has no available building sites, a crossed-out cube will appear over it.

Holding Shift will allow the new fragment to be attached over an existing bond, rather than creating a new one. This works even for atoms that have no available building sites, but do have existing bonds. While holding Shift, tapping Ctrl allows the bond that will be replaced on the target atom to be selected. Both the anchor atom on the fragment and the atom at the other end of the target bond are removed when the fragment is placed.

Finally, since fragments may have many different attachment points, Alt cycles over the possible attachment points on the current fragment.

To define new fragments, see the section on defining fragments.

Delete

Operates in a similar way to the Draw tool, except that clicking on an atom deletes it, and click-dragging over a bond deletes it.

Transmute

Clicking on individual atoms transmutes them into the current Element. Long-pressing exposes an option to transmute all atoms in the current selection.

Add H

Clicking on individual atoms adds on hydrogen atoms until the basic bond order requirements of the atom are satisfied. The algorithm attempts to find the best geometry for the new hydrogens as it can. Long-pressing exposes options to add hydrogens to all atoms in the current selection, or all atoms in the current model.

Grow

The Grow tool allows individual atoms of the current Element to be added ('grown') to clicked atoms. Long-pressing allows selection of the desired geometry in which atoms should be added, along with control over the distance of added atoms (either Use van der Waals Radii or a set Fixed Distance). There also exists the option of growing an atom, in the specified geometry, onto each atom in the current selection.

Add Atom

Allows addition of atoms into the current model at specific normal or fractional coordinates.

Element

The Element button allows specification of the element for newly-created atoms by selection from the periodic table.

Prevent Fold

When transforming atoms in a periodic system with the mouse (i.e. rotating or translating them) if any move outside the unit cell as a result of the transformation they are automatically folded back in to the confines of the cell. If Prevent Fold is enabled these folding operations will not occur.

Keep Centered

If the Keep Centred option is enabled, any editing operation will trigger a 're-centering' of the current model, so that the centre-of-geometry of the model being edited is always at the origin. This can be useful when editing non-periodic models, and keeps everything nice and centered on the screen.

Bonding Group

Bonding Group

Rebond

Recalculates all bonds in the current model, determining whether two atoms are bound from the relative, scaled radii of the atoms involved. The default mode (single-click) is to determine connectivity between atoms and then perform a subsequent augmentation of the detected bonds (i.e. attempt to resolve multiple bonds, aromaticity etc.). See the topic on bonding for a description of how these algorithms operate. Long-pressing exposes options for recalculation of bonds without augmentation, and for restricting the recalculation to the current selection or to make use of the current pattern definition. The tolerance of the algorithm may also be adjusted - a higher tolerance means more bonds will be detected, but may potentially detect unwanted connections.

Augment

Applies the augmentation algorithm to the current model, keeping the current connectivity as-is.

Clear

Removes all bonds from the current model. Long-pressing exposes options to remove bonds only from the current selection.