A. When reprocessing data at the data station, you MUST type the spectrometer name followed by a return before you start. Valid choices for spectrometer names are AC200 or AM360

B. Typing RESET followed by a return before you start will make your output more reproducible. Any of the parameters set by this command may then be changed if you like.

A. A COSY spectrum in a sample changer run called RUNN will have created the following data files for sample number nnn:

RUNN0F.nnn - FID of normal proton acquisition

RUNN0S.nnn - Fourier transformed spectrum of RUNN0F.nnn

RUNN1nnn.SER - Raw data of 2-D COSY acquisition

RUNN1nnn.SMX - Fourier transformed spectrum of RUNN1nnn.SER

(These names assume that the COSY was the first experiment selected for this particular sample. The integer following "RUNN" is the experiment number for the particular spectrum (or FID). If one other spectrum was run prior to the selection of a COSY, the names would be RUNN1F.nnn, RUNN1S.nnn, RUNN2nnn.SER, and RUNN2.SMX. These correct integers can be determined from the filename listed on the plots. The above filenames will be assumed throughout the rest of this discussion.)

B. The contour plot produced by the sample changer automated run will have the filename for the transformed 2-D data, RUNN1nnn.SMX, as the first item in the parameter list.

C. The name of the file used for the F1 and F2 projections on the automated plot will be PROJH1.001. This is a scratch file that changes every time another 2-D experiment is run with the sample changer. Do not use the file PROJH1.001 for reprocessing at a later time because it will not necessarily contain your data! Sometimes the transformed data are stored on the disk as RUNN0S.nnn which may be used for replotting the contour plot with projections. In the event that RUNN0S.nnn was not stored, you will have to regenerate the transformed spectrum to be used as the projection and store it prior to proceeding to the 2-D plotting. See next step.

D. If RUNN0S.nnn was not stored during the sample changer run, regenerate it and store it with the following steps:

A. Read in all the data, 1-D, and 2-D parameters with the following sequence:

RE RUNN1nnn.SMX

PJ RUNN1nnn.SER

RP2D RUNN1nnn.SMX

B. If you had to create RUNN0S.nnn, check that the value for SR1 and SR2 in the 2-D data is equal to the value for SR in RUNN0S.nnn.

C. The transformed data may be viewed in contour by typing AP2D return. Use the + and - buttons to the left of the keyboard to set the level of the contours to remove unnecessary noise, yet display the peaks of interest. The A knob will move the cursor horizontally and the B knob will move it vertically. The upper left corner of the display will give the ppm values of the limits of the contour displayed and the current position of the cursor. To obtain an expansion of a region of the contour, type L and a box will appear on the screen which may be moved around with the knobs which have the following assignments.

Type X to make that box full scale on the display. Type ESC X (ESC followed by X, not simultaneously typed) to exit from AP2D. The level and limits of the display at the time you exit from AP2D will be used for the contour plot.

D. Start the plot of the contour with projections on both axes with CP2P followed by a return. Input RUNN0S.nnn for the filenames of both projections. (It can be very useful to display on the screen the contour plot as it will come out on the plotter. This can be done by changing the parameter DSPL to 1. All plots in the job where DSPL=1 will be routed to the screen until DSPL is set back to 0.)

E. If you do not plan to archive the data, delete all the data files associated with this acquisition, i.e. RUNN0F.nnn, RUNN0S.nnn, RUNN1nnn.SER, RUNN1nnn.SMX (created by XFB), RUNN1nnn.SMX0 (created by AP2D if you displayed the contour plot), RUNN1nnn.SMX1 (created by AP2D if you displayed an expanded contour plot).

A. The main differences between replotting a HETCOR or a COSY are that the spectra to be used for the projections are different and the references for the two axes are different.

B. In addition to RUNN0F.nnn and RUNN0S.nnn there will be RUNN1F.nnn and RUNN1S.nnn files and the 2-D data will be in files RUNN2nnn.SER and RUNN2nnn.SMX. The comments about processing the 1-D spectra in section II. C and D. above also apply to the 1-D data for the additional projection.

C. Follow the steps in section III. above except:

A. It is not necessary to archive the .SMX file. If an appropriate 2-D parameter file is stored with the .SER file, the transformed data can be readily obtained. The 2-D parameters for the sample changer run will have been stored in the 2-D parameter file RUNN1Z.nnn (or RUNN2Z.nnn for HETCOR). If you changed any 2-D parameters during your processing (e.g. apodization parameters, tick marks on the Y-axis, etc.), you can re-write the 2-D parameter file with those new parameters with WJ2D RUNN1Z.nnn. Make sure you do this from the job where you were doing the 2-D processing and that you have not read in any other data or parameters in this job since then. Delete .SMX, .SMX0, and .SMX1 files from the disk.

B. If there were 1-D parameters that you changed while processing (e.g. tick marks on the X-axis, offset, etc.), you can store them in the .SER file now while you have them in mind with the following sequence:

RE RUNN1nnn.SER

WR RUNN1nnn.SER

Again, make sure you do this from the job where you were doing the 2-D processing and that you have not read in any other data or parameters in this job since then.

C. Transfer the data to be archived (i.e. RUNN0F.nnn, (also RUNN1F.nnn for HETCOR), RUNN1nnn.SER, (or RUNN2nnn.SER for HETCOR) and RUNN1Z.nnn (or RUNN2Z.nnn for HETCOR)) to the VAX via Ethernet.

D. After your data have been archived, delete all the data files associated with this acquisition from the disk as soon as possible since 2-D data sets use a fair amount of disk space.