So as to be able to assign atom names to your resonances, you need to tell Analysis what molecules you are investigating. First of all you generate a Molecular System (as you may have more than one molecule in your NMR tube) to which you then add molecules (so-called Molecular Chains). The Molecular Chains are in turn generated from Molecule Templates. Inclusion of proteins/DNA/RNA is extremely straight forward and will be described here. Support for unusual amino acids and other molecules is in the process of being added. In the mean time if you contact the CCPN team via the mailing list they can probably help you include other molecules into your project.
To create a molecular system go the Molecules pull-down menu and select Molecular Systems. Click on Add Molecular System and give it a name.
To add molecules first edit the molecular templates by clicking Edit Molecular Templates or select Edit Molecular Templates from the Molecules pull-down menu. Click on Add a New Molecule and give it a name.
If you are adding a Protein (or DNA/RNA) click on Add Polymer Residues and type or copy/paste your sequence (making sure that the correct type of polymer is selected above). Select the cyclic polymer box if necessary. Click OK.
Back in the Molecular Systems pop-up you can now select your molecule template (next to arrow in centre panel) and click Make Chain from Template. Give it a chain code (usually this will simply be A, but if you have several molecules in your molecular system you should give them different chain codes, e.g. ‘A’, ‘B’ etc.). 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.
If your sample contains other NMR observable molecules, add these to your molecular system, too.