Tricks and Tips
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Operations can be reverted by pressing Undo/Redo / buttons on General toolbar.
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Paste names, InChi, CAS numbers directly onto the canvas, they will be converted into chemical structures right away.
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The easy way to modify or add new properties to an atom/bond/selection to right click on it and use an option from the pop up menu.
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You can introduce any kind of element and a lot of query features from Periodic Table dialog. Try out the Advanced panel as well.
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Use build-in structure templates, choosing Insert>Template Library from menu.
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Import peptide, DNA, RNA sequences from menu Edit>Source.
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Simple paste IUPAC name from Structure>Structure to name menu; you can add IUPAC numbering as well (menu View>Advanced>Atom numbering>IUPAC numbering)
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Calculate chemical properties like pKA, logD, Solubility using the options of Calculation menu (additional license needed).
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Is your molecule chemically correct? Check it pushing Check Structure button from General toolbar.
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Press Ctrl+2 (or Ctrl+3) if you want to clean your molecule in 2D (or 3D ).
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Check your molecule in online databases (Chemicalize, Chemspider, Pubchem) from File menu of MarvinSketch.