ChemComp import

You can create your own chemical compounds (chemComps) in CCPN by importing PDB files (with CONECT records), .mol files or .mol2 files (recommended!) with the FormatConverter

• 1. Start the FormatConverter as stand-alone or from Analysis via M:Other:FormatConverter.

  2. In the FormatConverter, go to M:Import:Single Files:Chemical Compounds and select the appropriate format.

  3. Click on [Select file], pick the file to be imported, and press [IMPORT].

  4. A window should now pop up with information about the compound you just imported.

  5. Give your compound a sensible ccpCode - this has to be unique and cannot overlap with existing ccpCodes from the library of compounds we provide.

  6. Add any other information you want to include. Leave the molType as 'other' at the top.

  7. Press [OK].

  8. A window will now pop up with the atom information

  9. In this window, you have to make sure that the atom names (the first column) are unique. You can also reset the element symbol of an atom, set the chirality and whether the atom is water exchangeable. Press [Update] after you make changes.

  10. If you're happy with the info, press [OK].

  11. A window will pop up asking you for a descriptor. This is a CCPN-specific code to distinguish between variants of a chemComp (protonation state, ...). Just leave this as 'neutral' (even if it's charged), and press [OK].

  12. An 'Add/change descriptor' window will pop up. Press [No].

  13. Save your project (M:Project:Save), the new chemComp will be saved along with it and should now be accessible in Analysis (a restart might be necessary).

Should you want to re-use this chemComp in other projects, you can copy it from the <projectName>/ccp/molecule/ChemComp directory into the same directory for the new project. Alternatively copy it into the CCPN installation <ccpnmr>/data/ccp/molecule/ChemComp directory so that it's always accessible (though this might create problems with major updates).