The Structure menu holds the chemistry commands and the document’s structure display settings. Items are listed here in the order they appear. A toggle shows a check mark when it is on. Settings marked “per document” are saved with the file, and the defaults given are those of the built-in presets.
Most commands are also in the command palette (Ctrl+K).
Display
| Item | What it does | Covered in |
|---|
| Aromatic Display: Kekulé | Switches aromatic rings between alternating double bonds and a circle. The label shows the current mode (“Kekulé” or “Circle”). Per document; Kekulé in Traditional and Compact, Circle in Textbook. | Structure Settings |
| Show Lone Pairs | Shows or hides every lone pair. Per document; on by default. | Lone Pairs |
| Show Radicals | Shows or hides every radical electron. Per document; on by default. | Radicals |
| Bond Colors by Element | Colors each half of a bond with its atom’s element color. Per document; off by default. | Structure Settings |
| Show Carbon Labels | Writes “C” on carbon atoms. Per document; off by default. | Structure Settings |
| Show Implicit Hydrogens | Writes implicit hydrogens into atom labels. Per document; off by default. | Structure Settings |
| Show Orbitals | Shows or hides every orbital lobe. Per document; on by default. | Orbital Tool |
| Hybridization Tools (Experimental) | Shows the hybridization orbital tools. On by default for new documents. | Orbital Tool |
| Auto-Clear Orbitals from Labels | Keeps orbital lobes clear of atom labels. Same setting as Clip at Label; on by default. | Structure Settings |
Atom Numbering
| Item | What it does | Covered in |
|---|
| Show Atom Numbers | Shows or hides atom numbers. | Atom Numbering |
| Auto-Number Atoms | Numbers the selected atoms in the order you selected them, or every atom when nothing is selected. | Atom Numbering |
| Clear Atom Numbers | Removes numbers from the selected atoms, or from all atoms when nothing is selected. One undo step. | Atom Numbering |
| Number Style… | Opens a dialog for the color, size and font of atom numbers. | Atom Numbering |
Orbital Picture
| Item | What it does | Covered in |
|---|
| Build Orbital Picture | Draws the orbitals of the selected atoms, or of the whole drawing, using the choices below. | Orbital Pictures |
| Remove Orbital Picture | Removes the orbital picture. | Orbital Pictures |
| Draw: Full Picture / p Orbitals Only | Draws hybrid lobes, lone pairs, shared pairs and pi bonds, or only the p orbitals and what joins them. | Orbital Pictures |
| Ink: Colour / Black and White | Draws the lobes in the document’s orbital colours, or with dark outlines and grey shading. | Orbital Pictures |
| Spacing: Automatic / As Drawn / Cozy / Roomy | Sets the bond lengths of the picture. Automatic keeps them as drawn unless they are too short, then uses Cozy (1.5 times as long). | Orbital Pictures |
| Join p Orbitals: Ribbon / Single Line / Dashed Line / Nothing | Sets what joins the p lobes of a pi bond. | Orbital Pictures |
| Join the Far Side Too | Also joins the lobes on the far side of the bond. | Orbital Pictures |
| Delocalized Pi Systems | Draws a pi system of three or more atoms as one system, joined over every bond in it. | Orbital Pictures |
| Hide Covered Far Lobes | Leaves out the far half of an out-of-page p orbital where the lobes in front would mostly cover it. | Orbital Pictures |
Stereo labels and validation
| Item | What it does | Covered in |
|---|
| Show Stereo Labels | Shows or hides R, S, E and Z labels. | Stereo Labels |
| Assign R/S, E/Z | Has no effect in the current version. | Stereo Labels |
| Clear Stereo Labels | Has no effect in the current version. | Stereo Labels |
| Show Validation Warnings | Shows or hides validation markers and the status-bar badge. Same as the Toggle Validation Warnings button in the action bar. Per document; on by default. | Validation |
| Validate Structure… | Opens the Validation panel listing every issue, and turns the markers on if they were off. | Validation |
| Clean Up Structure | Moves atoms toward standard bond lengths and angles. One undo step. | Validation |
| Straighten Bonds | Puts bonds that are up to 2 degrees off a 15 degree line (3 near horizontal or vertical) exactly on it, in the selected molecules or in all of them. Other bond angles do not change. One undo step. | Bond Tool |
Views and resonance
These commands work on a selected molecule. When one cannot apply, the item is dimmed and its tooltip gives the reason.
| Item | What it does | Covered in |
|---|
| Derive View > Lewis, VSEPR, Condensed, Bondline, Fischer Projection | Draws a copy of the selected structure in that view, to the right of the original. One undo step. | Views and Resonance |
| Derive View > All Applicable | Draws every applicable view not already present and groups them with the original into a visual set. | Views and Resonance |
| Set Category > Lewis, VSEPR, Condensed, Bondline, Fischer | Tags the selected drawing as that kind of depiction. | Views and Resonance |
| Set Category > Clear Category | Removes the tag. | Views and Resonance |
| Generate Resonance Forms | Adds the other resonance forms of a symmetric ion such as carbonate or nitrate, joined by resonance arrows. | Views and Resonance |
| Generate Octet Resonance Forms | Writes the octet-respecting ionic forms of an expanded-octet species such as SF6 or XeF4. | Views and Resonance |
Text, names and settings
| Item | What it does | Covered in |
|---|
| Import SMILES… | Opens a dialog that turns a SMILES string into a drawing. | SMILES |
| Copy as SMILES | Copies the selection as a SMILES string. | SMILES |
| Copy IUPAC Name | Copies the name shown in the status bar, which is PubChem’s common name. | PubChem Names |
| Copy Structure Description | Copies a plain-text summary: counts, formula, SMILES and, when fetched, the IUPAC name. | SMILES |
| Spellcheck | Turns the browser spellchecker on or off in text editing. Per document; on by default. | Text |
| Structure Settings… | Opens the Structure Settings dialog. | Structure Settings |
To import a MOL, SDF or XYZ file, use the File menu; see MOL and SDF Import and XYZ Import.
See also
