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BMRB Import

BMRB Import

Note that this is new for Version 3.1 - in older Versions the import is slightly different

You can import a Chemical Shift List from a BMRB NmrStar file by dragging an NmrStar file into your project (make sure the file extension is .str), going to File / Import / NmrStar File and selecting a file, or typing BI and selecting a file. A pop-up will appear asking whether you want to Import the file or open it as a New Project. Select whichever fits your situation. The Import from NmrStar pop-up will then show you all the different elements contained in the BMRB file. Any elements which can be imported are shown in black with a tick next them, other elements are greyed out. Currently, the only parts of a BMRB file which can be imported are the Entry Information (imported as a Note), the Sequence (often denoted by the protein name in the BMRB file) and assigned chemical shift lists. Select or deselect the parts of the NmrStar file you want to import as appropriate. If you are importing a sequence or chemical shift list, you can set the letter used for the NmrChain and Chain in your project using the drop-down menu provided. Finally, click on Import to import the data. This process may take a minute, especially for medium to large sized proteins. When it is finished, your project should contain a new Note, if you imported the Entry Information, a new Chain if you imported the Sequence and new ChemicalShiftList and NmrChain (containing the NmrResidues and NmrAtoms that are in the new ChemicalShiftList) if you imported an assigned chemical shift list.

Creating a Spectrum Peak List

If you want to create a peak list from your imported chemical shifts, then you can do so after importing the shifts. Go to your imported Chemical Shift List in the sidebar and right-click and select Simulate Spectrum. Give your new Spectrum a name and then select what type of spectrum you would like it to be. At the moment we are limited to 1D 1H, 2D 1H-15N HSQC, 3D HNCO, 3D HNCA, 3D HNCOCA and 3D HNCACB spectra. Click on Create and the program will create a new dummy spectrum with your chosen name. This contains the peak list from the imported chemical shift list. You can copy this peak list to a real spectrum, simply by dragging it onto that Spectrum in a SpectrumDisplay. Later you can delete the dummy spectrum if you like. If desired, you can make your new imported peak list distinct by changing its colour: simply double-click on the peak list in the sidebar to bring up the Peak List Properties dialog and choose new colours for the peak symbols and labels.

Known Issues

Not all BMRB files are in the latest 3.2 NmrStar format. Some files are still in the 3.1.1 format which stops the assigned chemical shift lists from being recognised by CcpNmr Analysis. (The NmrStar version a BMRB file is in is indicated near the top of the file.) A fix for this is to make a couple of manual adjustments to the file following the examples below:

Find the Assigned chemical shift lists section of the file. Near the start of this section change the highlighted parts of following three lines from something like:

save_chemical_shift_assignment_data_set_one
   _Assigned_chem_shift_list.Sf_category       assigned_chemical_shifts
   _Assigned_chem_shift_list.Sf_framecode      'chemical_shift_assignment_data_set_one'

to:

save_assigned_chem_shift_list_1
   _Assigned_chem_shift_list.Sf_category       assigned_chemical_shifts
   _Assigned_chem_shift_list.Sf_framecode      assigned_chem_shift_list_1

Or they may look something like this:

save_chem_shift_list_1
   _Assigned_chem_shift_list.Sf_category       assigned_chemical_shifts
   _Assigned_chem_shift_list.Sf_framecode      chem_shift_list_1

In which case, change them to:

save_assigned_chem_shift_list_1
   _Assigned_chem_shift_list.Sf_category       assigned_chemical_shifts
   _Assigned_chem_shift_list.Sf_framecode      assigned_chem_shift_list_1

The chemical shift list import should now work.