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Creating Chains with Non-canonical Amino Acids

Creating Chains with Non-canonical Amino Acids

Note that this is a new feature introduced in Version 3.2.2

ChemComps

When you create a protein Chain in CcpNmr AnalysisAssign, the program will base this on a set of amino acid template files. These template files are so-called ChemComp files, written in xml format. They contain information about the amino acid's atoms, bonds, protonation states, names, codes, magnetic equivalent groups, prochiral groups etc. If you want to create a Chain which contains a non-canonical amino acid, you will therefore need a ChemComp file describing it. You can find out how to find or create such a file in our information on Creating Non-canonical Amino Acid ChemComps.

Importing a ChemComp .xml file

You can import a ChemComp .xml file either by dragging and dropping it into your project or using File / Load Data (shortcut LD). The file will then be saved in the my_project.ccpn/ccpnv3/ccp/molecule/ChemComp directory of your project and be available to you at any point when you are using that project.

Ccp Codes

When adding your protein sequence, you have the choice of using either the standard One-Letter Code format (A for alanine etc.), the Three-Letter Code format (ALA for alanine etc.) or using the Ccp Code format. In order to add non-canonical amino acids you will need to use the Ccp Code format. For the standard amino acids the Ccp Code is simply the three letter amino acid code in Title Case: Ala, Arg, Asn, .... For amino acids whose ChemComp files you have downloaded from our ChemComp repository on GitHub you need to use the three character code in the file name following protein+. So, for example, for 3-chloro-4-hydroxyphenylglycine, the ChemComp file name is protein+Chp+msd_ccpnRef_2007-12-11-10-20-11_00013.xml and so the Ccp Code is Chp. The Ccp Code is also given near the top of the file as ccpCode="Chp". For non-canonical amino acid ChemComps that you have created yourself in ChemBuild, the Ccp Code is the one you entered as part of the Compound Information. As for the other ChemComp files, it will also be in the .xml file name and near the top of the file.

Creating the Chain

In the sidebar, expand the Chain section and double-click on New Chain. Alternatively, select New Chain... from the Molecules menu. Fill in your options as normal. For the sequence you will need to use the CcpCode option. This can be a bit awkward, because you don't always have the sequence formatted as Met Tyr Pro Arg Thr Glu Ile Asn. So if you wish, you can copy and paste your sequence into the One-Letter Code tab and then right-click and select Copy all to Clipboard as Ccp Codes and then paste this into the Ccp Code tab, inserting your non-canonical amino acid Ccp codes at this point.

Note that you can use the little number button to tidy and verify your sequence or the orange back arrow to go back to plain text.

Finally, click on OK. Your new Chain will be created and your protein/peptide will be added to the project as a Substance.