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Importing a Sparky Project

Importing a Sparky Project

Analysis V3 contains a simple Sparky importer. Since Sparky projects don't always follow a completely standard setup, we cannot guarantee that your project will be imported fully, but hopefully most of your data will be transferred into CcpNmr AnalysisAssign V3 correctly.

You can import a Sparky project by dragging & dropping a Sparky .proj file onto the sidebar or drop area. You can also drag & drop one or more Sparky .save files into Analysis.

Changing amino acid types from 1-letter to 3-letter code

Amino acid types in Sparky projects are often given in one-letter code. Analysis, by contrast, uses uppercase three-letter code (IUPAC and NEF convention). In order for Analysis to recognise your assignment correctly, your assignments must specify the amino acid types in three-letter code. We have included a simple macro which will allow you to convert your amino acid types from one- to three-letter code. To run the macro, go to Macro / CCPN Macros and select ConvertNmrResiduesOneToThreeLetterCode. Any NmrResidues with amino acid types in 1-letter code will be converted to 3-letter code. Please note that this macro runs fairly slowly - the terminal output will show your progress.

Moving peak assignments into a single NmrChain

Depending on the setup of your Sparky project you may find that you have lots of different NmrChains in your Analysis project - one for each spectrum and one for the resonance list. You will encounter the same situation if you have imported several .save files. You can move all your NmrResidues into a single NmrChain using a macro provided by CCPN. Go to Macro / CCPN Macros and select MovePeakAssignmentsToMoleculeChain to run it. All your NmrChains will be merged into a single NmrChain called molecule which you can then rename by double-clicking on it in the sidebar.

Known issues

November 2019 - we are aware of several issues which may cause problems when importing a Sparky project. For example, the presence of 'QB'-style pseudoatoms will prevent the project from opening and peak lists are not always imported correctly. We are currently working on fixes for these issues.