A manual is found on Andy's software page, and will print to screen if you just type pipp.

The 3D input files have to be named with extension .DAT in caps.
Get a copy of the pipp.com file to run the program.
Edit the base name of the input files (generally data/testxyz), the base name for the output files (4 files will be output encompassing the peak pick table), the S observe freq. for Z the SW in Z and the number of slices
(get first two from fid.com, number of slices is number of testxyz files.  I set z start and end to 1 and 128.
Set appropraite printer name
Run pipp by typing pipp.com

If the program doesn't run, but instead complains that the desired values for contour limit and multiplier do not match the binary values, this is because these values were changed by "c" "t" "e" or "c" "m" "e" the last time the program was run.  Just re-edit the last line of the pipp.com file to make the values mentioned there match the binary values mentioned in the error message.  It is possible to avoid this annoyance by editing the first line to setenv CNTR_IGNR_BIN_FL 1; however,
this slows down the display of planes when stepping through the planes.
 

When the program is run, there is a spectrum window and a status window.  Keep the cursor over the spectrum window.  For commands that require text entry, the entry line will appear on the top of the status window.  The cursor has to be over the spectrum window to type in the status window.

General order of event for developing a peak table from a 3d dataset:

Jump to the slice in which to commence work.  Type j; in status window fill in slice number (no decimal point), or z dimension in ppm (with decimal point).

To enter a signal into the peak table with a name, type n to get into "name peak" mode; left click the spot on in the spectrum; fill in the name on the status window command line.  The name will appear over the spot on the spectrum.  When you toggle out of "name peak" mode with "n", a list of peaks picked only for this slice will appear in the status window.  A comprehensive table (.PCK) will appear in directory when the program is exited (with "e").  The name, slice number, coordinates, and intensity are recorded.  The names would generally come from an HSQC for which the signals had been previously assigned arbitrary numbers as names, thus facilitating matching them up between experiments.  To make an entry without a name, left click without going into name mode first.  Remove errant entries by right clicking the spot.

Use ^W often to output and update this table during a session (because the program is known to crash).  Move up or down one slice at at time with up and down arrows (down arrow moves up in slice number).

Finer points of entering a peak:

Left clicking enters the Z coordinate of maximum intensity in a process that estimates the maximum to a point between the planes.  If the slice with the greatest intensity wasn't active, a "+" or "-" will be entered instead.  These "+" and "-" values are hidden when you print the peak pick table. You have to navigate to the maximally intense slice  to mark and name the signal. The left click also shifts the X and Y positions of the label to the peak top.  Often you will want to mark a position of a shoulder that isn't at a peak top in one of the dimensions.  Then you have to right click, which marks exactly on slice and at the X and Y position of the cursor.

A right mouse click removes an entry from the table, but also attempts to identify the label to remove by interpolating in X,Y, and Z.  In practice, you are better off to control right click to avoid removing the wrong labels.  Control right click should remove the label directly under the cursor, whether it was put there by interpolation or not.  If Control right click doesn't work, you have to zoom in and make sure the cursor is within the label box when you control right click.

To see if a spot is maximal in the z dimension, or merits labeling as a shoulder in the z dimension, activate a z trace with "z".  This will interpolate to the peak top in the x and y dimensions, and then display a curve for the z dimension with a blue dot where the slice intersects.  If you then change planes, the curve will remain and the blue dot will migrate to the point of intersection of the new plane.  This is a convenient way to navigate to the peak top in the z dimension.  The display unzooms when you change planes, but you can just follow the blue dot on the z trace, and then rezoom with "d" when you hit the peak top.  You can look for a shoulder in the X or Y dimension that has a different maximum in the Z dimension by using control left click in Z trace mode to see the Z trace for the point exactly under the cursor.  It is convenient to hunt for overlapping peaks by control left clicking in z trace mode at several points within an extended spot.  The point displayed by the blue dot on the Z trace is also marked as a blue square on the 2D display. Up to the last 7 clicked points in z trace mode are marked by white dots in the 2D display.  This is a convenient way to transiently mark one or more spots and then track them as you change the zoom level.  Also, when z trace is on, the labels go away.  During remote access, this is a better way to toggle the labels than using the space bar.  Z trace will stop working after 8 points are marked, and a message about "no trace selected" will appear in the status window.  At this point, you must press delete or backspace to erase the stored coordinates before continuing to use z trace.  Also, the position of the curve within the window appears to depend on where the cursor was when backspace and z were last executed.  So if the curve is too close to the top or bottom, try putting the cursor someplace by trial and error and doing the backspace, "z" maneuver.

There are also horizontal and vertical trace modes turned on by "v" and "h" and off by "e".  They don't usually show mich more than is obvious by looking at the contours, although they can clarify that a shoulder in the contours is really too small to be a companion peak.  "v" trace is often useful for just drawing the vertical base line as a vertical straight edge to see if two well separated spots are really lined up.

Two addtional techniques help with crowed spectral regions:

1. toggle the labels off with <space>
2. zoom in on a region by middle clicking the center of it; expanding or reducing the zoom box with left and right mouse clicks; then effect the zoom with a 2nd middle click.  "f" takes you back to a full scale display.  Holding down "h" or "v" while rescaling the zoom box will limit the rescaling to horizontal or vertical dimensions, respectively.
3. For resolving adjacent intense peaks, reduce the contour multiplier by "c" "m" <new value> "e".