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Adding the Structural Formula

You can easily paste a ChemDraw picture, or drag it into an iNMR window. It may be more convenient, although a little more complicated, to import, instead, a mol file (or any other of the recognized formats) that describes the same structure.

If there is a standard installation of Open Babel on your Mac (see below), the structure (mol file) is imported instead of the picture. Open Babel can generate a mol file from ChemDraw data, but not from picture files!

Advantages of Importing a Mol File:

Step 1

[Mac-only] When you import a structure into a document, iNMR extracts the elemental formula, the SMILES description and the molecular weight. This information is indexed by Spotlight, showed by the Finder command “Get Info” and can later be used to search the spectrum.

Step 2

You can show or hide the carbon and hydrogen atoms and the atom numbers.

Step 3

You can change the font.

Step 4

When you print the document or generate a picture, the resolution of the structure will always be the same as the resolution of the spectrum.

Step 5

If you know the definition of a mol file, you can edit the atom labels.

Step 6

[Mac-only] Using an external application, like BBEdit, you can recreate the mol file or create a high-quality Quartz image from the note. In the first case, drag the note into a .txt document; in the second case, drag the note into an .rtf document (use copy & paste if you don't like drag & drop). Regardless of its spectroscopic use, you can adopt iNMR as an helper for those applications (e.g.: MarvinSketch) that let you create great structures but not great pictures.

Extra for Mac

OpenBabel a suite of free command-line programs. Installing them is incredibly easy and we recommend you to do it. There are other packages, also free, that already contain OpenBabel: iBabel and ChemSpotlight. iNMR assumes a default installation (the programs “babel” and “obprop” are installed into /usr/local/bin) and calls OpenBabel to perform some of the actions described in this page.

If you have installed OpenBabel but don't want iNMR to use it (for example: you want to import a ChemDraw picture exactly as it appears inside ChemDraw) uncheck the command Edit > Call Open Babel.

Related Topics

Modifying an Existing Note

Storing Metadata

 

Web Tutorial

Manipulating a mol file