Edit detail for ImportingAnXeasyProject revision 1 of 1
1
Editor: damberger
Time: 2009/04/03 15:58:35 GMT+0
Note: 
changed:
-
Importing an XEASY project (updated to include work with Start1.2.cara)

 Note: if you are NOT a former XEASY user who wants to transfer a project into CARA, you can skip this and go on to ImportingTemplate

   1. "Import a template":ImportingTemplate into a repository (or start with a repository already containing a library of !ResidueTypes,!SpectrumTypes etc).

     If the template is derived from Start1.2.cara (which uses BMRB nomenclature) you need to convert the XEASY files to BMRB nomenclature as follows:

     - Execute the script *!XeasySeqToThreeLetter.lua* found in either the Terminal-pane of CARA-Explorer or "here":ScriptsToConvertExternalFiles. (see the "CALUA page":CaLua for how to load and run scripts) and select the sequence file: script will write out a BMRB compatible seq file. Import this seq file in step 2 below. 

     - Execute the script *!XeasyToBmrBLabelsInProtonList.lua* and select the protonlist file. Script will write a BMRB compatible protonlist file. Import this protlist file in step 4 below.

   2. Use *Project > Import > Project from Sequence ...* to import a XEASY-type .seq file. In almost all cases the contents represent residues, not spin systems, so answer accordingly in the following dialog box.

   3. A new project has been created, it carries the name of the sequence file. Choose Sequence inside of the new project to display the sequence.

   4. Now import an XEASY atom list (.prot). Since this list is associated with a project, Right-click on the project name in the main window and select *Project > Import > Atom List ...*

   5. Check your imported atoms in the project's Spins pane or in the Spin Systems pane. Clicking on a Spin System puzzle piece expands it to show that systems spins.

   6. Now add a spectrum. Go to the Spectra entry in the main window and right-click in the right-hand window. Select *Add Spectrum* and then a spectrum type corresponding to your spectrum. (E.g. select HSQC15N) and then select the data file of the spectrum (currently Cara nmr, Bruker rr, Xeasy param, !NmrPipe ft, Sparky ucsf and Felix mat formats are available).

   7. You can associate this spectrum with an XEASY peak list. Unlike an atom list, a peak list is linked to a given spectrum. Open the spectrum using *Open !MonoScope* from the right-click menu. Then within MonoScope use *Peaks > Import Peaklist ...*. If necessary rotate or calibrate your peaklist using the commands *Peaklist > Rotate* or *Peaklists > Calibrate*.

   8. In the main window, click the Peaklists entry to see all your peaklists and the dimensions they have. Peaklists are provided for backward compatibility, you will not benefit from all CARA-features by using them exclusively.

   9. Open HomoScope on a 2D or PolyScope on a 3D spectrum. Assuming you possess a repository with correct spectrum type definitions, you will see a dynamically generated peaklist for this spectrum and atom list. For backward compatibility with XEASY, you can use *File > Export > Peaks to MonoScope* to export this peaklist and send it to MonoScope where you can edit it further there (Integrate, Save ...). If you plan to continue your work in CARA use the advanced SystemScope / SynchroScope / StripScope windows for your work.

  10. If you want to display NOE crosspeaks on a NOESY in HomoScope proceed as follows: Open the NOESY with MonoScope. Import the NOESY peaklist. Select *Peaks > Import !SpinLinks* (Use the default values in the dialog window). Close MonoScope (You do not need to save the peaklist). Now open the NOESY in HomoScope. You should see all the expected NOE crosspeaks. For 3D NOESY: Do the same thing using PolyScope.

  11. If there are differences in the position of spins in different spectra, you can introduce aliases for the shifts in a given spectrum as follows: Open the spectrum with MonoScope. import the peaklist of the spectrum with *Peaks > Import Peak List*. Create the spin aliases with *Peaks > Import Aliases*. Now the position of the spins in HomoScope will reflect the shifts from the peaklist. This is not advised for assignment projects since you assume the shifts are the same in different spectra when matching chemical shifts.

Importing an XEASY project (updated to include work with Start1.2.cara)

Note: if you are NOT a former XEASY user who wants to transfer a project into CARA, you can skip this and go on to ImportingTemplate

  1. Import a template into a repository (or start with a repository already containing a library of ResidueTypes,SpectrumTypes etc).

    If the template is derived from Start1.2.cara (which uses BMRB nomenclature) you need to convert the XEASY files to BMRB nomenclature as follows:

    • Execute the script XeasySeqToThreeLetter.lua found in either the Terminal-pane of CARA-Explorer or here. (see the CALUA page for how to load and run scripts) and select the sequence file: script will write out a BMRB compatible seq file. Import this seq file in step 2 below.
    • Execute the script XeasyToBmrBLabelsInProtonList.lua and select the protonlist file. Script will write a BMRB compatible protonlist file. Import this protlist file in step 4 below.
  2. Use Project > Import > Project from Sequence ... to import a XEASY-type .seq file. In almost all cases the contents represent residues, not spin systems, so answer accordingly in the following dialog box.
  3. A new project has been created, it carries the name of the sequence file. Choose Sequence inside of the new project to display the sequence.
  4. Now import an XEASY atom list (.prot). Since this list is associated with a project, Right-click on the project name in the main window and select Project > Import > Atom List ...
  5. Check your imported atoms in the project's Spins pane or in the Spin Systems pane. Clicking on a Spin System puzzle piece expands it to show that systems spins.
  6. Now add a spectrum. Go to the Spectra entry in the main window and right-click in the right-hand window. Select Add Spectrum and then a spectrum type corresponding to your spectrum. (E.g. select HSQC15N) and then select the data file of the spectrum (currently Cara nmr, Bruker rr, Xeasy param, NmrPipe ft, Sparky ucsf and Felix mat formats are available).
  7. You can associate this spectrum with an XEASY peak list. Unlike an atom list, a peak list is linked to a given spectrum. Open the spectrum using Open MonoScope from the right-click menu. Then within MonoScope use Peaks > Import Peaklist .... If necessary rotate or calibrate your peaklist using the commands Peaklist > Rotate or Peaklists > Calibrate.
  8. In the main window, click the Peaklists entry to see all your peaklists and the dimensions they have. Peaklists are provided for backward compatibility, you will not benefit from all CARA-features by using them exclusively.
  9. Open HomoScope on a 2D or PolyScope on a 3D spectrum. Assuming you possess a repository with correct spectrum type definitions, you will see a dynamically generated peaklist for this spectrum and atom list. For backward compatibility with XEASY, you can use File > Export > Peaks to MonoScope to export this peaklist and send it to MonoScope where you can edit it further there (Integrate, Save ...). If you plan to continue your work in CARA use the advanced SystemScope / SynchroScope / StripScope windows for your work.
  10. If you want to display NOE crosspeaks on a NOESY in HomoScope proceed as follows: Open the NOESY with MonoScope. Import the NOESY peaklist. Select Peaks > Import SpinLinks (Use the default values in the dialog window). Close MonoScope (You do not need to save the peaklist). Now open the NOESY in HomoScope. You should see all the expected NOE crosspeaks. For 3D NOESY: Do the same thing using PolyScope.
  11. If there are differences in the position of spins in different spectra, you can introduce aliases for the shifts in a given spectrum as follows: Open the spectrum with MonoScope. import the peaklist of the spectrum with Peaks > Import Peak List. Create the spin aliases with Peaks > Import Aliases. Now the position of the spins in HomoScope will reflect the shifts from the peaklist. This is not advised for assignment projects since you assume the shifts are the same in different spectra when matching chemical shifts.