So as to be able to assign atom names to your resonances, you need to tell Analysis what molecules you are investigating. Do this by selecting Molecule Setup in the Molecules menu. You can add a protein, DNA or RNA sequence to Analysis and it will automatically generate the full molecule for you. It will also create a so-called Molecular System. Your Molecular System should contain all relevant molecules in your NMR sample. If you are just looking at a single protein then this is the only molecule that needs to be included in the Molecular System. But perhaps at a later stage you will also investigate your protein in complex with a another protein or a ligand. You will then need a second Molecular System for the complex since this will have different chemical shifts, a different structure and could require some new assignment work. Unusual amino acids and other molecules can also be added to your molecular system. Go to the Small Compounds tab in the Molecule Setup pop-up to do this or contact the CCPN team via the mailing list for help with how to include other molecules into your project.

To add your protein (or DNA/RNA) click on the Add Sequence tab and type or copy/paste your sequence into the box (making sure that the correct type of polymer and 1/3-letter code is selected above). You can also read the sequence in from a file using the Read File button at the bottom of the pop-up. Make use of the other options at the top of the pop-up if you need to: select the Cyclic box if your protein is cyclic. If it does not start with residue number 1, then simply enter the correct residue number for the first amino acid in your sequence into the Start Number box. Or if you are adding a second squence to a Molecule or Molecular System, then select the relevant Destination Molecule or Destination Mol System from the drop-down menus. Now click Add Sequence! at the bottom of the pop-up.

You will be asked for a New Molecule Name – it is usually helpful to choose something meaningful such as the name of the protein. Then you will be asked for the Molecular System Code – MS1 will do, but choose something else if you like. Finally you need to a specify a Chain Code – A is usually a good choice for your first molecule. For proteins you will be asked whether the Phe/Tyr Hd1/2 and He1/2 atoms are equivalent due to rotation or not. In the vast majority of cases these aromatic rings have sufficient space to be able to rotate and the Hd1/2 and He1/2 atoms will thus end up with identical chemical shifts. There are some molecules where rotation is hindered. Unless you know this to be the case for your molecule, simply click Yes.

Note that the other tabs in the Molecule Setup pop-up now contain various bits of information about the molecule you have just entered.

If your sample contains other NMR observable molecules, add these to your Molecular System, too.