yes, it is possible to work with non-standard amino acids, but it isn`t very streamlined at the moment.
As regards chains: you can enter your sequence in 3-letter code, e.g. ALA VAL ILE SER THR and then simply add in a the code for your non-standard amino acid at the appropriate point in the sequence. However, that will only work if you have the ChemComp file for that amino acid in your library of xmls (in /src/python/ccpnmodel/data/ccpnv3/ccp/molecule/ChemComp) - otherwise it won`t recognise the 3-letter code. There is a library of non-standard AA ChemComps available on Github at https://github.com/VuisterLab/CcpNmr-Che...mp/protein . In principle you can also build your own non-standard AA in ChemBuild and then import a ChemComp from there, but it needs some manual tweaks at the moment - some bugs we haven`t yet fixed. Get in touch with us directly at firstname.lastname@example.org if you want more details.
Once you`ve got your chain, however, it is slightly limited in what you can do with it - I think you can create NmrAtoms, but it isn`t yet set up for NEF export and other things like that. Luca is currently working on sorting some of these things out.
But it depends a bit on what you actually want to do and whether you will really need all of this.
Remember that you can always create your own NmrChains in whatever way you like, so you can label and assign your peaks without having an official "Chain" in your project (in contrast to V2). If you want to have a full NmrChain in your project before you make assignments (rather than creating the NmrChain/NmrResidues/NmrAtoms as you go along), then the easiest thing is probably to create a chain with something like Ala`s where you have non-natural AAs, create your NmrChain from that and then change the NmrResidues which are non-natural.
Happy to provide more details if you like.