Chem Illustrator

Keyboard Shortcuts and Tips

. Free software under the GNU General Public License, version 3 or later.

Hotkeys work like ChemDraw: point at an atom or bond (it highlights blue) and press a key. A key that grows something moves the highlight to the new atom, so you can keep typing (8 then 1 makes an E double bond). 1 and 0 keep the highlight under the mouse, so pressing 1 three times adds three bonds; after a click or another key they move it, so 1 1 1 draws a chain. Every key can be changed.

Pointing at an atom

    Pointing at a bond

      Pointing at empty space

        Drawing tools

        • Text tool: click to type a caption; the bar above the text has bold, subscript, formula style, Greek letters and symbols. Esc finishes
        • Arrows, shapes and brackets are in the tool bar; drag their handles to change them, and use the Style panel for line width and color
        • Templates (rings, heterocycles, amino acids, sugars): click empty space to place one, a bond to fuse it on, an atom to join it there
        • Format menu: align, distribute, flip, rotate, scale and join; or drag the round handle above a selection to turn it. Arrow keys nudge the selection; adds a reaction arrow and a copy of the selection to turn into the product
        • Chemistry menu: Clean Up Structure evens out bonds and angles while keeping stereochemistry; Fixed Bond Lengths and Fixed Angles can be turned off (or hold Alt while drawing)
        • Insert > Structure from Name or SMILES () draws a structure from its name: systematic (IUPAC) names, CAS-style names and many common names such as caffeine or ethyl acetate. A CAS RN (50-78-2) works too: its check digit is checked, then it is looked up in your Compound Library, numbers found before, and PubChem (NCI CACTUS when PubChem doesn't know it). Other names it can't read, such as trade names, are looked up on PubChem. Select a caption holding a name first to replace the caption with the structure. Names are read on this computer by OPSIN, so it works offline. Substituent names such as 4-methoxyphenyl get a wavy-line point of attachment
        • Insert > Structure from Sequence draws a peptide from its one-letter (GLYPHS, small letters for D) or three-letter sequence (Boc-Ala-D-Phe-OMe), with the N- and C-terminal groups you pick. The Sugars and Nucleic acids palettes hold Haworth sugars, bases, nucleosides and nucleotides

        Drawing styles

        • File > Drawing Style… sets how structures are drawn in the tab showing: bond length, line widths, double-bond spacing and label fonts. Built in are ACS 1996 (every ACS journal), RSC, Nature journals and a larger Slides style, with the source of each set of numbers shown. Every number can be changed
        • Save as My Style keeps your changes under a name, in every mode. Check Use this style for new … to make new canvases, presentations, designs, documents or spreadsheets start in it
        • View > Reading Mode (or the eye button at the top) shows the page dark: black ink as light gray, white paper as dark gray, colors dimmed. It changes the screen only; files, printing, copies and exports stay as they are. View > Window and Colors > Reading Mode Colors… picks Graphite, Slate or Warm dark, or your own paper and ink colors
        • When there are structures already, choose Redraw (they take the new bond length and widths) or Keep their look (only new structures use the new style). One Undo puts it all back

        Chemistry checks

        • Red boxes mark atoms with too many or too few bonds, labels that can't be read, and atoms sitting on top of others. Point at one to see why; the Warnings panel lists them all, with Ignore. Chemistry > Check Structure goes to the next one. They are never printed, saved or copied
        • Rest the mouse on an abbreviation or condensed label (OTBS, NHBoc, CO2Me) to see the group written out, with its name and formula. View > Chemical Abbreviation Tooltips turns this off.
        • Axial chirality (biaryls, allenes, alkylidenecycloalkanes) gets Ra or Sa by IUPAC P-93.5.1: draw the groups on one end of the axis with a wedge and a hash (or one wedge) to show which way around it is. Edit > Settings writes them as P/M instead.
        • R/S and E/Z are worked out for every structure as you draw. Chemistry > Show Stereo Labels adds them to the selected structures (or all) as part of the drawing; they update by themselves after edits. Select a stereocenter to hide its label or type your own (for example (R*)). View > Show R/S Preview shows every label in red on screen
        • As in ChemDraw, plain bold bonds count as wedges and plain hashed or dashed bonds as hashed wedges. Where R or S would depend on what an R or Ar group is, no label is given

        Everywhere

        • Mouse wheel scrolls, Ctrl+wheel zooms, middle or right drag pans; the View menu zooms too
        • Copy puts the selection (or the whole drawing) on the clipboard; in the Windows app it pastes into ChemDraw, and into Word and PowerPoint as a picture. Paste takes drawings from ChemDraw, and SMILES or molfile text
        • File menu: New Canvas, New ▸ Presentation, Spreadsheet, Document or Design, Open, Save and Save As (.cdxml, .cdx, .pptx, .xlsx, .csv, .sdf), Export PDF, Export Molfile. Each file has a tab; Ctrl+Tab moves between them. You can also drop files on the window

        Spreadsheets

        • Excel's keys and formulas (SUM, AVERAGE, ROUND, IF…). Chemistry > Structure draws a structure in a cell; paste one from ChemDraw too. Double-click a structure to change it
        • Properties adds columns that work out formula, MW, exact mass, HRMS m/z, cLogP, TPSA and more from each structure; =D2/MW(B2)*1000 gives mmol. Type over any value; Reset to Calculated puts it back
        • Sort and Filter work on any column; By Substructure shows the rows whose structure contains a part you draw

        Documents

        • Pages like Word's (Letter, 1 inch margins, Times New Roman 11 to start): the ribbon has Word's tabs and keys (Ctrl+Alt+1 Heading 1, Ctrl+Enter a new page, Ctrl+E center…)
        • Styles: Normal, Title, Heading 1 to 3 and Caption. Change a style in the panel on the right and every paragraph in it changes, except what was formatted by hand
        • Insert > Structure draws a structure in the text; double-click it to change it, drag its corner to size it. Paste from ChemDraw too. Insert > Document > Caption numbers figures, schemes and tables by itself, and Cross-reference puts "Figure 2" in the text, which follows the caption
        • References > Manage References keeps the document's references: add one by DOI (filled in from Crossref), by hand, or from a BibTeX or RIS file, and choose the style (ACS, Angewandte, RSC). Insert Citation puts superscript numbers in the text, given in order of first citation (double-click one to change it); Bibliography lists the references cited. Any value can be changed by hand, and a reference's bibliography text can be typed over
        • Layout: paper, margins and page numbers (S1, S2… for Supporting Information); the panel has the header and footer

        Not in this prototype yet

        • Rings bonded to a metal through all their atoms (ferrocene)