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BMRB Import

BMRB Import

You can import a Chemical Shift List from a BMRB file by dragging an NmrStar file into your project (make sure the file ends in .str), going to Project / Import / NmrStar File or typing BI. A pop-up will appear showing whether the BMRB file contains an assigned chemical shift list or not. If it does, this will have a little tick beside it and you can click on Import to import the assigned chemical shifts. This process may take a minute, especially for medium to large sized proteins. When it is finished, your project should contain a new chemical shift list and a new NmrChain containing the NmrResidues and NmrAtoms that are in the new chemical shift list.

Creating an HSQC Peak List

If you want to create an HSQC peak list directly from your imported chemical shifts, then you can do so by ticking the Simulate Peak List option. Now type N,H in both boxes and click on Import. As well as importing your chemical shifts, the program will create a new dummy spectrum named NH. This contains the HSQC peak list from the imported chemical shifts. You can copy this peak list to your HSQC simply by dragging it onto an HSQC spectrum display. Later you can delete the NH dummy spectrum if you like. If desired, you can make your new imported HSQC 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.