Processing 2D data using VNMR

[written by Dave Fuller and Bosong Xiang]

 

Phase-sensitive experiments that produce pure absorption line shapes

 

A. phase-sensitive NOESY, TOCSY, ROESY, HMQC(not with gradients)

 

1.          pmode='full'                    this allows you to phase the data in the t2 dimension after the full 2D transform.

 

2.                                    set fn and fn1.  fn   np, and fn1   2*ni

 

3.       wft(1)          or ft(1)          transforming the first fid should produce the one-dimensional spectrum in these types of experiments.  Phase the spectrum as you would any one-dimensional spectrum by clicking on the phase menu item and choosing a high-field peak to adjust the zero-order phase paramter (rp) and then clicking on a low-field peak to adjust the first-order parameter (lp).

4.          wtia(1)                    interactively select and adjust a weighting function.  A Gaussian function is appropriate for these types of experiments.  The purpose of the weighting function is:

1.      Zero-filling results in a truncated fid.  The weighting function will force the fid to decay to zero smoothly, therefore,  reducing sinc wiggles in the transformed spectrum.

2.      maximize S/N and resolution.

          Click on the gf menu button to adjust this parameter with the left mouse button.  Choose the value that will smooth your data without causing too much line broadening. Click on the gfs menu button and adjust this value also with the left mouse button.  This narrows your peaks at the base.  Too large of a shift will produce negative peaks at the base of your positive peaks and will produce strange looking crosspeaks in the 2D spectrum.  Check your phasing by typing wft(1).

5.          wft1da                    Fourier transform the t2 dimension. 

 

The partially transformed data are called interferograms and should be displayed on the screen.  If a matrix containing the data isn't shown, type dconi.  If the horizontal axis isn’t labeled t1 type trace=’f1' dconi.  Adjust the number of intensity levels by clicking on the intensity scale with the middle mouse button.

 

Click on the trace menu item with the left mouse button.  Move the crosshair with the left mouse button and select a slice(interferogram) that contains signal.  Remember this index number which is printed on the top of the screen or leave the crosshair at this position.

 

6.       wtia or wtia(index)          Interactively select weighting function for the t1 dimension.  Again, a Gaussian function is appropriate.  Adjust gf1 and gfs1 as you did in step 4 for the t2 dimension. 

         

7.          wft2da                              The computer will now apply the specified weighting functions and will perform a Fourier transform on both dimensions.

 

8.       dconi will display the 2D matrix and allow you to interactively adjust the number of intensity levels.  dpconi will display contour levels.  Adjust the vertical scale by setting the value of vs for the best representation of the data.  You can also use the menus for this: main menu   display   colormap or contour.

 

9.          Phasing the t1 dimension:

 

Click on the trace menu item and use the left mouse button to select a trace with a diagonal peak at the high field end of the spectrum.  Save this index number by typing r1=index no.  Next, select a slice with a low-field diagonal peak and save this index number in r2.  To view the first slice type ds(r1).  Make sure you are in the center of the peak you'd like to phase by first setting r6=r1 and then typing n (for next) to display slice r6+1 or l (for last) to display slice r6-1.  Once you find the diagonal peak with the maximum intensity type r1=r6.  For the low field diagonal peak set r6=r2 and ds(r2).  Use n and l to find the center of the peak and set r2=r6.  To phase ds(r1).  Click on the phase menu item and click on the peak you'd like to use for your zero-order phase correction.  Phase this peak by adjusting rp with the left and right mouse buttons.  Leave the cursor pointed at this peak so you don't move the position where you apply the zero-order phase correction.  Type ds(r2) and press the F6 function key for phasing.  Without moving the mouse, click the left mouse button, now you can move the mouse to click on the lowfield peak to phase.  Adjust the first-order phase correction and click on box when finished.  dconi will display the phased spectrum.

 

10.     Go to section C-E for referencing, plotting and saving.

 

B. phase-sensitive COSY; DQCOSY; MQFCOSY

 

1.          pmode='full'          this allows you to phase the data in the t2 dimension after the full 2D transform.

2.          trace='f2'                    sets x-axis to t2

 

3.                                    set fn and fn1.  fn   np, and fn1   fn/2

 

4.          df2d(1)                    display raw fids

 

5.       dconi                     display data with interactive contour levels; click on the trace menu item to select a slice with sufficient signal for weighting and phasing

          For coherence transfer type experiments, unlike NOESY-type, little signal is present in the first fid, therefore, you must read in a slice at a later t1 point such as fid # 100.

Remember the slice # you choose (specified by index at the top of the screen) or leave the cursor at that particular slice.

6.          wtia(s#)                    perform interactive weighting on slice s#; you don't have to enter the index number if the cursor is placed on the slice you want.  Just type wtia without moving the cursor.  Adjust weighting function appropriately.  A Gaussian function is recommended for phase-sensitive data which is chosen by clicking on gf and gfs and adjusting with the cursor.  See section A.4.

7.          wft1da                              Weight and transform the t2 dimension.  Follow section A.5 for selecting an interferogram to use for weighting in the t1 dimension.

 

8.       wtia or wtia(s#)          With cursor on slice or s#=no. of slice.  A Gaussian function is also recommended here.  Adjust gf1 and gfs1.

 

9.          wft2da                              Perform weighting and two-dimensional transform. 

 

10.         Phasing both dimensions:

 

          trace='f2'                    Read in slice that contains cross peaks at high-field end of spectrum for setting your zero-order phase parameter.  Phase antiphase crosspeaks to have equal intensity for the positive and negative peaks.  Read in a slice with low-field crosspeaks for setting the first order phase parameter.

          trace='f1'                    Do the same as in the previous step for the t1 dimension.

 

C. Referencing

 

Place the cross hair on a crosspeak that you would like to use for referencing.  Reference the F2 dimension by typing rl(#p) where # represents the chemical shift in ppm and reference the F1 dimension by typing rl1(#p).  If the indirectly detected dimension is heteronuclear such as C13, type rl1(#d).

 

D. Plotting

         

You can zoom in on part of the spectrum by creating a box.  The left mouse button move the lower left corner of the box and the right mouse button creates and moves the upper right hand corner.

 

          pcon(8,1.4)                    generates a hardcopy contour plot with 8 contour levels and the 1.4 represents a good value for the spacing of these levels.

 

E. Saving parameters

 

If you retrieved a saved file before processing, the string file should contain your filename.  You can check this by typing file?.  If the name is correct type svf(file) and respond y and all of your processing parameters will be saved with your raw data.  If you don't want to overwrite this file, you can save the parameters in a .par file by typing  svp(filename).  After retrieving your data, load this .par file before processing.  Typing wft2da will produce your 2D data file processed with these saved parameters.  Before transforming type pmode='' for faster processing, but you will not be able to readjust any phasing parameters.

 

If you have any questions please see Ivan or Tony.