Using PROG_PATH /S1/Apps/Dan/bin
/s/Apps/DanBin/pipp.sgi5 help
Documentation: pipp.help Program: pipp.c
Date Editted: November, 1997 Purpose: Interactive Peak Picker
See Also: ps_contour.help, By: Dan Garrett
contour_sim.help and capp.help


Program requires a minimum of three arguments:

pipp <Data File> <Abs. Threshold> <Level Multiplier>

Optionally may also specify Starting and Ending chemical shifts:
<X Start> <X End> <Y Start> <Y End> <Z Start> <Z END>
where X and Y values are in PPM unless value is appended with a H or a h and Z
values are in slice number. All other options controlling the start of the
peak picker are set through shell environment variables defined in a shell
script, e.g. pipp.com, that calls the executable. The environment variables
are described below. The use of environment variables for parameters will
end with this release of PIPP.

Do NOT invoke the program using
source pipp.com
as this will pass the environment variables from the pipp.com shell back
to the parent shell (ie the variables become defined in your window).
Make the pipp.com file executable as in:
chmod +x pipp.com
and then execute using:
pipp.com


The <Data File> is the file name for the 2D, 3D or 4D NMR data files
which may be stored in a single file or a series of files in which each
file has a single 2D plane or 3D cube. Each file must have a 512 float
parameter header followed by a series of 32 bit floating point numbers
consisting of only the real points. If the NMR data are stored in a
series of 2D files then <Data File> should be the base name to the files
ie HNCA. The format for file names for a 3D experiment stored as a series
of 2D files is the base name appended with a three digit number indicating
the slice number (ie third dimension data point) with the extension .DAT,
ie HNCAzzz.DAT. The format for file names for a 4D experiment stored
as a series 2D files is the base name appended with a two digit number
indicating the fourth dimension data point and a three digit number indicating
the third dimension data point with the extension .DAT, ie HNCAaazzz.DAT.
The <Abs. Threshold> is the minimum absolute value for calculating contours.
The <Level Multiplier> specifies the separation between successive contour
levels to give exponentially increasing levels.


**** Notes Specific to PIPP ****

Pipp is a primitive interactive peak picker based on the X window system
utilizing the Sun XView (Open Look) Tool Kit. Since there are 2 layers
of graphic libraries ( XView and X), pipp does NOT always behave as desired.
For instance, if you attempt to type ahead of the display, the display may
freeze up and you will have to login on another terminal and kill your process.
Another frustrating problem is that sometimes the keyboard is not responsive.
This usually occurs when the mouse pointer wanders into one of the text
windows. Keaping the mouse pointer out of these windows helps prevent this
problem. There are two ways that we have found to wake-up the keyboard:
(1) point the cursor at a blank region of the spectrum and hit the Left Mouse
Button as if to add a peak, or (2) slowly move the mouse pointer over the
title border of the contour window. Lastly, if you are sharing the computer
with other users pipp will run more slowly than if you are the only user, be
patient and watch the Status Window, typing ahead will only increase your
blood pressure.

The peak pick table that pipp uses is eithor taken from the base name of the
spectra or specified through the variable PK_FILE_NAME. However, capp creates
two ASCII peak pick files: one for the user in a tabular form, and a second
for pipp in which a peak pick syntax is used to define the peaks. The first
form has the extension .PCK, the second form has the extension .ASG. It is
strongly recomended that immediately after capp is run you make a backup of
both the .PCK and the .ASG file. Pipp can read eithor the .PCK or the .ASG
format, BUT unless an environment variable is set ONLY the .ASG version will
be read (see PK_TABLE_FORMAT). If the .PCK file is editted you must set
PK_TABLE_FORMAT to 1 so that pipp will read in the .PCK file. Note the .ASG
file contains information about peaks whose intensity is greater on adjacent
slices (ie the + and - symbols seen in pipp).

Some operations in pipp require only a single keystroke to initiate a command.
Other operations require further information, such as a slice number (or shift),
before the operation can be completed. Upper and lower case is NOT
distingiushed in pipp and some operations have a few equivalent keystrokes.
The table below shows the keystrokes, ie commands, that are recognized by
pipp enclosed in single quotes (you do NOT enter the single quotes). For
alphanumeric commands only the lower case is shown in the table, however
upper case may also be used. For non-alphanumeric keystrokes, i.e. clicking
a mouse button, hitting the space bar, or hitting an arrow key, the keystroke
is spelled out in upper case.

The commands are divided into groups depending on the Input Mode of pipp. The
current input mode is always shown in the tile border or the status subwindow.
The default Input Mode is the Peak-Pick Mode in which many operations are
performed. From the Peak-Pick Mode a single keystroke will put pipp in the
other input modes which are: Look-Only Mode, Name Peak-Pick Mode, Inform Peak
Mode, 2-Contour Mode, Strip Man. Mode, Zoom Set Mode, Jump Mode, Contour Level
Setting Mode, XY Trace Mode, and ZA Trace Mode. While in a specific Mode
only the keystrokes available to that Mode will be accepted by pipp. Note
that some keystrokes perform the same operation in different Input Modes while
other keystrokes have diferent operations depending on the Input Mode. If
you find any discrepencies between this document and the
working of pipp please let me (Dan Garrett) know about it via E-Mail,
dgarrett@speck.niddk.nih.gov.

Note: Although the Shift key is not used to modify commands, the
Control key and the Diamond are used to modify the behavior of commands.
Use of the Control key will be written with the circumflex, ^. For example
Control-W is written as ^W. Use of the Diamond key will be written as DMD-.
For example Diomond-j is written as DMD-j, which mean while holding down
the Diamond key press the j key. SGi computers will use the Alt key in place
of the Diamond key.

When PIPP prompts for information a default value may be shown in paranthesis
which can be accepted by hitting the return key.

The Esc key is used to exclusively to get out of a mode, command or prompt
without changing anything.


**** Interactive Commands ****


**** Peak-Pick Mode and Contour Peak-Pick Mode ****

Keystroke Description

'e', 'q' To quit the program. The current Peak pick table will
be saved in two files, ie the .PCK and the .ASG file,
prior to program exitting.
'^R' To read a Peak Pick Table from disk.
You will be prompted for the base name of the file.
Depending on the value of PK_TABLE_FORMAT eithor the .PCK
or the .ASG file will be read in. PK_TABLE_FORMAT can NOT
be interactively changed at this time.
'^W' To write the current Peak Pick Table without exitting program.
You will be prompted for the base name of the files.
Two files are written to disk, one with the extension .PCK
and the second with the extension .ASG. The previous
contents of the files are overwritten.
'DMD-R' To Read in an assignment table.
'DMD-W' To Write in an assignment table.
You will be prompted for the name of the assignment
table to read/write.
'SPACE' To toggle display of peak annotation. Space bar toggles
between peak annotation being displayed or not.
If the environment variables controlling annotation,
ie peak ID #, box around peak or peak lable, are turned
off then the space bar will do nothing.
'MS-LEFT' To add a peak to the peak pick table using X, Y interpolation.
Click Left Mouse Button when the cursor is pointing to
the peak that you want to add to the table. By default the
X, Y and Z chemical shifts are Interpolated around a
nearby local extrema. Interpolation can be overridden by
using the control key. If the intensity at the interpolated
chemical shift is greater on the previous or the next 3D
or 4D slice than a +, -, ++, or -- symbol will mark the
peak. The program will not automatically add a peak to
another slice. It is up to the user to look on the other
slice and determine if the peak is real or an artifact.
Use 'DMD-MS-LEFT' as described below to Move a peak.
'MS-RIGHT' To remove a peak from the peak pick table using X, Y
interpolation. Click The Right Mouse Button when the
cursor is pointing to the peak that you want to remove
from the table. By default the X and Y chemical shift is
interpolated around a nearby local extrema prior to
removing the nearest peak. The interpolation can be
overridden using the control key.
'CRTL-MS-LEFT' To add a peak to the peak pick table without X, Y interpolation.
While holding down the Control Key click the Left Mouse Button
when the cursor is pointing to a peak to be added to the
Peak Pick table. No X,Y interpolation is performed, the
exact location (limitted by the screen resolution) of the
cursor determines the X, Y chemical shift of the peak. The Z
chemical shift will be interpolated only if the intensity
is greater on this slice than on the previous or next 3D slice.
Warning messages will be sent to the status window if the
intensity at this chemical shift is greater on the previous or
the next slice. It is up to the user to check the other slices
to determine which slice the peak truly belongs in. The best
way to remove a non-interpolated peak or any peak that is not
located at or near the peak extrema is with a controlled remove.
'CRTL-MS-RIGHT' To remove a peak from the peak pick table without X, Y
interpolation. Click the Right Mouse Button when the
cursor is pointing to the peak that you want to remove
from the table. No X, Y interpolation is performed.
This is the best way to remove peaks from the table
that are not near a local extrema. Also this is the
only way to remove peaks that are over signal lower
than the contouring threshold.
'DMD-MS-LEFT' To Load Peak information (ie Pk-ID, label and assignment) from
a nearby Pk-ID that is close to the top of the peak so
that the Peak information can be moved to a new location.
Note that the cursor will change and that the top border
to the window shows the Pk-ID that has been loaded.
The Mode remains the same and all commands (ie 'j',
'h', 'MS-MIDDLE', 'MS-RIGHT', etc) except adding
a peak work exactly the same. Anytime after the information
has been loaded the peak can be moved by pointing
the mouse to the new location and clicking 'MS-LEFT' which
then causes the peak to be deleted from the original
location and added to the new location.
As usual the 'Esc' key escapes from the current operation
which in this case unloads the peak information and keaps
the peak in the original (unmoved) location.
Note for users of TWM (Tab Window Manager) check your
~/.twmrc to make sure that the following is NOT set:
Button1 = m : window|icon : f.function "move-or-lower"
The above setting makes it impossible to use 'DMD-MS-LEFT'.
'CRTL-DMD-MS-LEFT'
Same as 'DMD-MS-LEFT' except that X, Y interpolation is
not used to find the peak to load information from.
'MS-MIDDLE', To initiate the Zoom-Set Mode. Click on the Middle Mouse Button to
initiate the Zoom-Set Mode. The Zoom-Set Mode is used for
interactively setting the region that is to be expanded.
Initially a Zoom Box that is 10% the size of the currently
displayed region is centered on the cursor. The user has control
over the size of the Zoom Box by changing this percentage only.
This is done so that the user can quickly specify the region
to expand without having to drag the edges or the center. As
the cursor moves the center of the Zoom Box follows the cursor.
'l' To initiate Look-Only Mode, ie does not use NMR data.
This is usefull to look at the contours on different
Slices without having to read in the NMR data files.
For Strips this is used for setting the length (or number)
of strips to be displayed.
'c' To initiate Contour level setting Mode.
'x' To initiate Trace mode for an X trace.
'y' To initiate Trace mode for an Y trace.
'z' To initiate Trace mode for an Z trace.
'a' To initiate Trace mode for an A trace.
The 2D plane being viewed may be taken from any two axis
of the NMR data, e.g X and Y; or X and Z; or Y and Z.
If the trace is for an axis parallel to the 2D plane
that is being viewd than a Plane-Trace Mode will be
initiated. If the trace is for an axis perpindicular to
the 2D plane being viewed than a Perp. Trace Mode will
be initiated. Only 1 Trace along 1 axis can currently
be viewed. And to change from viewing a trace along
a given axis to another axis the user must exit the Trace
Mode for the current axis and re-enter the Trace mode for
the new axis. Immediately upon entering Plane Trace
Mode a Trace along the desired axis will shown and can
be manipulated using the commands in Plane Trace Mode.
For Perp. Trace Mode the user must select using the
'MS-LEFT' key which perpindicular trace is desired.
Also in Perp. Trace Mode 8 Traces are kept in a buffer
for each perpindicular axis. If/when all 8 buffer trace
locations are filled the user may hit the 'DEL' key to
clear the buffer. Finally, in Perp. Trace Mode a filled
rectangle the size of the digital resolution marks the
position of the trace on the 2D plane, and a filled circle
around one of the trace points indicates which point
on the trace is in common with the 2D plane being viewed.
'h' To initiate Plane-Trace mode for a Horizontal trace.
'v' To initiate Plane-Trace mode for a Vertical trace.
The program determines which axis is running horizontal
or vertical before initiated Plane Trace Mode.
See comments above concerning Plane Trace Mode.
'f' To re-display the spectrum expanded to original dimensions.
'd' To go Down the display stack, ie a previously expanded region.
'u' To go Up the display stack, ie the most recently displayed
region. As expansion regions are defined in Zoom-Mode
using 'MS-MIDDLE' they are kept in a display stack.
'd' will go down the stack from a larger region to a
smaller region and 'u' will go up the stack from a smaller
region to a larger region.
'o' To toggle the screen Orientation, ie switch X and Y axis.
This will NOT change the NMR data, only changes how the
the data is displayed. Also this is not saved between
PIPP sessions, ie next running of PIPP will forget.
'g' To toggle display of the Grid, ie grid on or off.
't' To toggle between having the peak pick table displayed or not.
'p' To create a PostScript file of the currently displayed region
and spool to desired printer. You will be prompted for
the name of Printer for Spooling the plot. You can hit
the Esc key prior to hitting enter to escape from
plotting. Note there are many variables that are
described in ps_contour.help that are active for this
plot. Currently, there is no way to interactively
change the plotting parameters while in PIPP. As of
this version 1D Traces are NOT plotted. Although Peak
ID numbers are plotted, Peak name labels are NOT plotted.
'i' To toggle Inform Peak Mode on/off.
Inform gives information about a peak that was clicked
on without actually adding to the Peak Table. If
assignments are known then possible assignments are given.
Also PDB Structures may be used to limit possible
assignments in NOE experiments. Note: Specification of
PDB Files, type of Experiment and Error Ranges are done
in a parameter file (.par file). Use the environment
Variable STAPP_PAR_FL to specify the name of the .par file.
The .par file can have any name and extension, but for
convenience it will be simply called the stapp.par file.
'DMD-i' To toggle Std Out Peak Mode on/off.
This is very similar to Inform Peak Mode except that
the information is sent to stdout preceeded by the
what the environment variable STD_OUT_CMND is set to.
This was created to be a primitive way for
PIPP to communicate to a tcl shell script via the
unix pipe facility, ie pipp.com | script.tcl
When in Std Out Peak Mode the Pk ID, Intensity,
X_POS, Y_POS and Z_POS in PPM are sent to the
program script.tcl for processing. Note by holding
down the shift key while in Peak-Pick Mode or in
Inform Peak Mode the peak information sent to stdout.
'n' To toggle Name Peak-Pick Mode on/off.
Name gives possible assignments for a given peak an allows
the user to select one of the assignments while adding
the Peak to the Peak Table. If assignments are not known
then the user may enter any char string. Also PDB
Structures may be used to limit possible assignments in
NOE experiments. Note: Specification of PDB Files, type
of Experiment and Error Ranges in done in a parameter
file (.par file). Use the environment variable
STAPP_PAR_FL to specify the .par file. The .par file can
have any name name but for convenience it will be
called the stapp.par file.
'^F' To Change the Param ELL_FRACT_MIDL_LVL. This is only active
if the parameter ELL_PERC_MIDL_USE has been set and the
the parameter XVW_DSPLY_CTL is set to 1 in the pipp.com
file. Changing this affects the intensity that contours
are selected from to be used to define the peak position
when in Contour Peak-Pick Mode. To get in Contour
Peak-Pick Mode you must set the Environment variable
ELL_PERC_MIDL_USE. There is no interactive toggle between
Peak-Pick Mode and Contour Peak-Pick Mode.
'm' To initiate Strip Manipulation Mode. This mode allows the user
to manipulate the order of Strips. A strip is defined by
a pair of shifts, ie NH and N-15 for a 3D N-15 NOESY.
In order to use strips within pipp you must first generate
a 2D NMR data file of all the strips using Stephan
Grzesiek's program plot_seq, or your own program. Then
PIPP must be told which axis the strips are along with
the SP_AXIS environment variable. A future version of
PIPP will allow the dynamic creation of strips from
an incomplete assignment table or text file.
'DOWN-ARROW' To go to the next 3D slice (ie increase Slice ID by 1).
For Strips this is used to jump/scroll to the next
set of strips.
'UP-ARROW' To go to the previous 3D slice (ie decrease Slice ID by 1).
For Strips this is used to jump/scroll to the previous
set of strips.
'RIGHT-ARROW' To go to the next 4D slice (ie increase Slice ID by 1).
For Strips this is used to jump/scroll to the next
set of strips.
'LEFT-ARROW' To go to the previous 4D slice (ie decrease Slice ID by 1).
For Strips this is used to jump/scroll to the previous
set of strips.
'j' To initiate Jump Mode. Jump Mode is used for selecting which
slice is to be viewed. The reason that it is a mode
is that the user can not do other functions until a correct
slice has been selected or the escape key hit. The user
will be prompted for the number or shift for all axis
perpindicular to the displayed plane. Although the
prompt will come from the Status Window the mouse MUST
stay in the Contour Window as the user responds, ie
do NOT move the mouse into the Status Window. If the
two environment variables, STAPP_PAR_FL and SHIFT_FL_NM,
are set correctly then you can use known assignments to
jump to a residue by entering its single letter amino
acid code followed without a space by its residue number,
e.g. you can jump to the plane containing R31. For
Strips this is used to set the first strip displayed, ie
jumps from current first strip to another first strip.
The single letter amino acid code is ignored, and only
serves to distinguish jumping by slice and residue.
To Jump by Pk-ID number use `120 to go to Peak ID 120.
'DMD-j' To initiate Jump Mode by residue number or spin-system.
Note this requires that two environment variables,
STAPP_PAR_FL and SHIFT_FL_NM, be set so that known
assignments are used to jump. User may enter the residue
number only or the single letter amino acid code followed
by the residue number without a space. The single letter
amino acid code is not checked against the amino acid
for the residue number that was entered, e.g R31 may
actually be K31. But if the ASCII key entered if not
one of the defined amino acids then the integer is
used as a spin-system ID. See stapp.help for definition
of spin-system and it's use within the assignment table.
For 2D through bond exp, ie HSQC or HMQC, allows
jumping to different residues and display of
cross hairs via 'DMD-l' command.
'`' '\' To initiate Jump Mode for Pk-ID jumping. Note this is
same as regular jump except the ` or \ have
already been put into the jump string so that only
the Peak-ID followed by Enter needs to be typed.
If you delete the ` then you must re-enter it otherwise
PIPP will assume you are jumping by slice or shift.
'DMD-DOWN-ARR' To go to the plane that has the next residue on it.
Note this requires the same two environment variables
be set as in 'DMD-j' and requires that 'DMD-j' be used
first to define a current residue number before
scrolling to the next. If there is more than one plane
possible then you will be prompted for which plane to
jump to. The DOWN-ARROW key was chosen to mean an
increasing residue number because chemical shift tables
are written with lower residue numbers at top and higher
residue numbers at bottom. So you should picture a
chemical shift table with the arrow keys scrolling you
through the table. Also this definition is consistent
with scrolling by slice ID.
For 2D through bond exp, ie HSQC or HMQC, allows
scrolling to adjacent residues and display of
cross hairs via 'DMD-l' command.
'DMD-UP-ARROW' To go to the plane that has the previous residue on it.
Note this requires the same two environment variables
be set as in 'DMD-j' and requires that 'DMD-j' be used
first to define a current residue number before
scrolling to the next. If there is more than one
plane possible then you will be prompted for which plane
to jump to.
For 2D through bond exp, ie HSQC or HMQC, allows
scrolling to adjacent residues and display of
cross hairs via 'DMD-l' command.
'DMD-l' To toggle display of Assignment overlay lines.
These are lines on the 2D plane which show specific shifts
from the assignment table, ie the NH position for N-15
editted experiments. This also toggles showing in the
Contour border what residue/atom define the current plane.
'DMD-s' To change the SIAD control string.
The SIAD (Sequence Independent Atom Designator) control
string limits the possible planes and or assignment overlay
lines that will be found for the desired residue, ie
in a C-13 editted experiment the user can specify CA
instead of the default C* and will not be prompted for
which Carbon atom to use for each jump. The syntax for the
SIAD control string minimally contains an atom name for
each axis, but may also include residue types and
offsets. See SIAD_STRING definition in stapp.help. A
* for an axis means that you do not care about that axis.
If * is used for an axis on the plane being viewed than
lines will drawn for all atoms on that plane which match
the desired SIAD. Do NOT put an * for the perpindicular
axis.
Examples for several types of Experiments are shown below:
SIAD_STRING * HN N # For any N-15 Editted Exp.
SIAD_STRING * H* C* # For any C-13 Editted Exp.
SIAD_STRING H* * C* # For any Transposed
# C-13 Editted Exp.
SIAD_STRING HB*:+3 HA* CA # To see A,B (i,i+3)
# interactions
SIAD_STRING CA|CB:-3 HN N # For the CBCA(CO)NH Exp.
SIAD_STRING CA|CB:0|-3 HN N # For the CBCANH Exp.
Also look in stapp_exp.par for more SIAD_STRING examples.
'DMD-c' To toggle Complete Assignment Flag on or off.
See also STAPP parameter COMPLETE_ASGNMTS which sets
the initial value for the complete assignment flag.
's' To toggle showing all symmetry peaks when assignment table
is used. By default PIPP will only show symmetry
for each assignment in the assignment table that is
consistent with the selected peak in Inform or Name
Peak Mode. However, by turning the All Symmetry Flag
on PIPP will display in Inform and Name Peak Mode
all of the ND symmetry peaks in addition to the symmetry
for each assignment. This allows symmetry to be used
when only partial assignments are known and the correct
symmetry is currently unassigned.
'^I' To toggle Parabolic Interpolation of Peak Intensities on/off.
This makes very little difference if peaks are symmetrical
and there are enough points to define the peak. By default
the Intensity of the tallest peak is used when this if off.
See also INTERP_INTENS environment variable.


**** Inform Peak Mode ****

Keystroke Description
'ESC' 'i' To exit from Inform Peak Mode.
'MS_LEFT' To obtain Information about the Peak near the pointer.
Minimally the Chemical Shift of the Peak is written
to the Peak Table Subwindow. If 3D or 4D symmetry is
defined and required (see ^S below) then a list of
slices which have the symmetry are listed. Use '2' to
get 2-Contour Mode so that the current plane and symmetry
plane are displayed on top of each other. If assignments
are known then a list of possible assignments are given.
If Structural Models are known and the Experiment is
defined with an NOE Pair then the average distance found
among the structures is also listed for each assignment
which has at least one structure with the distance less
the maximum acceptable distance (see ^D below).
'^S' To toggle requirement of 3D or 4D symmetry. Symmetry can only
be required if the Experiment has been defined with
symmetry. Must set STAPP_PAR_FL and within the
stapp.par file must set EXP_NAME to an experiment that
has SYM_ATOMS set. See also stapp.help
'^E' To change the Error range for symmetry locator (in PPM).
Only 1 value is used for the 2 symmetry axis.
Make sure you hold the Control key before hitting 'e'
else you will exit pipp.
'^D' 'b' To change the maximum acceptable distance measured between
2 Atoms using potential assignments in an NOE Experiment
and a set of PDB files. This filters out assignments
between pairs of atoms with distance greater than limit.
Must be working with an NOE Exp and specify at least 1
PDB file. Must set STAPP_PAR_FL and SHIFT_FL_NM.

Inform Peak Commands that are the same as in the Peak Pick Mode.
The only difference between Peak-Pick and Inform are the addition
of the new commands and that Inform does NOT add to the Peak Table.
All of the commands that are available in Peak-Pick Mode except
'MS-RIGHT' are also available in Inform Peak Mode.

'MS-MIDDLE', 'p', 't', 'SPACE', 'j', 'DOWN-ARROW', 'UP-ARROW', 'RIGHT-ARROW',
'LEFT-ARROW', 'o', 'g', 'f', 'd', 'u', 'i', 'n', '2', 'e', 'q',
'^W', '^R', 'm', 'c', 'l', 'x', 'y', 'h', 'v', 'z', 'a'


**** Std Out Peak Mode ****

Keystroke Description
'ESC' 'DMD-i' To exit from Std Out Peak Mode.
'MS_LEFT' To send Information about the Peak near the pointer to stdout.
This is a very primitive way to have PIPP communucate
with another program, ie a tcl based script. The value
of the environment variable STD_OUT_CMND is written
on a single line with the following peak information:
-PK_ID, -INTENS, -IS_LCL_EXTRMA, -X_POS, -Y_POS, and
-Z_POS. If this becomes usefull more information
will be sent to stdout. In order for a separate
program to use this information the output of pipp must
be piped into the input of the other program as in:
pipp.com | script.tcl

Std Out Peak Commands that are the same as in the Peak Pick Mode.
The only difference between Peak-Pick and Std Out is that
'MS_LEFT' keystrokes create text sent to stdout.
All of the commands that are available in Peak-Pick Mode except
'MS-RIGHT' are also available in Inform Peak Mode.

'MS-MIDDLE', 'p', 't', 'SPACE', 'j', 'DOWN-ARROW', 'UP-ARROW', 'RIGHT-ARROW',
'LEFT-ARROW', 'o', 'g', 'f', 'd', 'u', 'i', 'n', '2', 'e', 'q',
'^W', '^R', 'm', 'c', 'l', 'x', 'y', 'h', 'v', 'z', 'a'


**** Name Peak-Pick Mode ****

Keystroke Description
'ESC' 'n' To exit from Name Peak-Pick Mode.
'MS-LEFT' To obtain Information about and Name the Peak near the pointer.
If assignments are not known then the user can only label
the peak (ie enter any arbitrary char string). If 3D or
4D symmetry is defined and required (see ^S above) then a
list of slices which have the symmetry are listed. If
assignments are known then a list of possible assignments
are given with an ID number that the user uses to select
the desired assignment. The user is immediately prompted
for an assignment and put into Assign Peak-Pick Mode. In
Assign Peak-Pick Mode the user can only select an
assignment or or hit ESC to escape. If Structural Models
are known and the Experiment is defined with an NOE Pair
then the minimum distance found among the structures is
also listed for each assignment which has at least one
structure with the distance less the maximum acceptable
distance (see ^D below).
If the STAPP parameter KEAP_DEG_PCK_ID has been set to TRUE
then the user can select multiple assignments seperated
by a space or a comma to define a degenerate assignment.
The label for the Peak will be set to "DEG-n" where n
will be the number of degenerate assignments for the peak.
The degenerate assignments are recorded in the file
with the suffix .DEG.
'MS-RIGHT' To remove a peak from the Peak-Pick Table and simultaneously
unassign it. If your desire is to simply re-assign
a peak it is NOT necessary to remove it first. To
re-assign a peak simply use 'MS-LEFT'.
'DMD-MS-LEFT' To Load Peak information (ie Pk-ID, label and assignment) from
a nearby Pk-ID that is close to the top of the peak so
that the Peak information can be moved to a new location.
See also description uner Pk-Pick Mode commands.
'^S' To toggle requirement of 3D or 4D symmetry. Symmetry can only
be required if the Experiment has been defined with
symmetry. Must set STAPP_PAR_FL and within the
stapp.par file must set EXP_NAME to an experiment that
has SYM_ATOMS set. See also stapp.help
'^E' To change the Error range for symmetry locator (in PPM).
Only 1 value is used for the 2 symmetry axis.
Make sure you hold the Control key before hitting 'e'
else you will exit pipp.
'^D' 'b' To change the maximum acceptable distance measured between
2 Atoms using potential assignments in an NOE Experiment
and a set of PDB files. This filters out assignments
between pairs of atoms with distance greater than limit.
Must be working with an NOE Exp and specify at least 1
PDB file. Must set STAPP_PAR_FL and SHIFT_FL_NM.


Name Peak-Pick Commands that are the same as in the Peak Pick Mode.
The only difference between Peak-Pick and Name Peak-Pick are the
addition/alteration of the commands shown above and that Name allows
the user to assign the peak.
All of the commands that are available in Peak-Pick Mode are also
available in Inform Peak Mode.

'MS-MIDDLE', 'p', 't', 'SPACE', 'j', 'DOWN-ARROW', 'UP-ARROW', 'RIGHT-ARROW',
'LEFT-ARROW', 'o', 'g', 'f', 'd', 'u', 'i', 'n', '2', 'e', 'q',
'^W', '^R', 'm', 'c', 'l', 'x', 'y', 'h', 'v', 'z', 'a'


**** Strip Man. Mode ****

Keystroke Description
'ESC' 'e' To Escape/Exit from Strip Man. Mode.
'^R' To Read manipilated order file.
'^W' To write manipulated order file.
You will be prompted for the name of the file to read in.
'1' To display the Original Order for the strips.
The Original Order is defined by the 2D NMR data file
which is created by Stephan Grzesiek's plot_seq program.
'2' To display the Manipulated Order for the strips.
The manipulated Order is defined in the manipulated order
file which has a list of the Strip IDs in the desired
order. The manipulated order may be changed using the
commands '^M', '^I', '^D' and '^S' described below.
'3' To display the Searched Order for the strips.
The searched order gets created whenever the '^P' command
is used to locate strips which have similar cross peaks.
'^M' To move a range of Strips from one location to another.
You will be prompted in the Table window for the
insert point. Click the Left or Right Mouse button with
the pointer between two strips to define the insert point.
The insert point MUST be in the Manipulated Order.
Next you will be prompted for the first and the last
Strip for the range of strips to be moved, no carriage
is neaded to effect the change. Click the Left or Right
Mouse Button with the pointer on the strip to be selected.
If the range to be moved is from the Manipulated Order
then the range of Strips is removed from the current
location and inserted in the new location. If the range
to be moved is from the Original then a copy of these
strips is inserted in Manipulated Order and the
Original Order is NOT changed.
'^I' To Insert a set of Strips into the Manipulated Order.
You will first be prompted in the Table window for the
insert point. Click the Left or Right Mouse button with
the pointer between the two strips to define the insert
point. The insert point MUST be in the Manipulated Order.
Next you will be prompted for the set of strips to be
inserted into the Manipulated Order. Click the Left or
the Right Mouse button with the pointer over each strip
to be inserted. You may use the 'DEL' key to remove
the most recent strip from the selection or you may use
'ESC' to escape. The strips being inserted do not nead
to be adjacent, but they must ALL come from the
Manipulated or the Original Order, ie can NOT use some
from Manipulated and some from Original Order.
You must hit the Return key to Insert the set of strips.
'^D' To delete a set of strips from the Manipulated Order.
You will be prompted for the set of strips to be deleted.
Use the Left or Right Mouse buttons with the pointer
over each strip to be deleted. As strips are selected
to be deleted they will be highlighted and their strip
ID listed in the Status Window. You may use the 'DEL' and
'ESC' key as in '^I' command. The strips being deleted
do not nead to be adjacent. You must hit the 'Return' key
have the set of strips deleted. Strips can NOT be
deleted from the Original Order.
'^S' To Swap any two strips. You will be prompted for the pair
of strips to swap. Click the Left or Right Mouse button
with the pointer over the two strips to be swapped.
At least one Strip MUST come from the Manipulated Order.
If both strips are in the Manipulated Order then after
after the second strip is selected the two are swapped.
If one strip comes from the Original or the Searched Order
than the Manipulated Order strip gets replaced by the
Original or Searched Order strip and the Original Order or
Searched Order strip does NOT change.
'^P' To Peak-Pick ALL extrema along a desired strip and enter
SM LOC ADJ Mode. SM LOC ADJ Mode compares the peaks
that have been picked on a single strip to ALL other
strips to determine i,i+1 or i,i-1 connectivities. See
SM LOC ADJ for commands that are used in this mode.
Click the Left or the Right Mouse button over the strip
to be Peak-Picked for the SM LOC ADJ mode.

Strip Man. Commands that are the same as in the Peak-Pick Mode.
Note the use of the Arrow keys and the 'l' and 'j' keys
for controlling which strips get displayed is part of
the definition of the dataset through the SP_AXIS and
and therefore works in all modes including the
Peak-Pick Mode.

'MS-MIDDLE', 'SPACE', 't', 'n', 'i', 'o', 'f', 'd', 'u', 'g', 'j', 'l',
'LEFT-ARROW', 'RIGHT-ARROW', 'UP-ARROW', 'DOWN-ARROW'


**** SM LOC ADJ ***

Keystroke Description
'ESC' 'e' To Escape/exit back to Strip Man Mode. There is no
difference between using 'Esc' or using 'e'.
'MS-LEFT' To add a Peak to the list used in locating
adjacent Strips. This is shown visually with an
X over the peak and a line extending to all the strips.
'MS-RIGHT' To delete a Peak from the list used in locating adjacent
strips.
'^C' To change the minimum number of Common Peaks between the
current strip and ALL the other strips. Default is 3.
'^L' To locate strips which are adjacent to the strip which
has been peak-Picked. The Strips are arranged
in order of decreasing number of Peaks in common.
Also listed in the Table window are the Strips which
matched a minimum number of peaks.
'^M' To Move a range of strips into Searched Order. Use in
same way as in Strip Man. Mode.
'^I' To Insert a set of strips into the Searched Order.
Use in the same way as in the Strip Man. Mode.
'^D' To Delete a set of Strips in the Searched Order.
Use in the same way as in the Strip Man. Mode.
'^S' To Swap a pair of Strips in the Searched Order.
Use in the same way as in the Strip Man. Mode.

SM LOC ADJ. Commands that are the same as in the Peak-Pick Mode.
Note the use of the Arrow keys and the 'l' and 'j' keys
for controlling which strips get displayed is part of
the definition of the dataset through the SP_AXIS and
and therefore works in all modes including the
Peak-Pick Mode.

'MS-MIDDLE', 'SPACE', 't', 'n', 'i', 'o', 'f', 'd', 'u', 'g', 'j', 'l',
'LEFT-ARROW', 'RIGHT-ARROW', 'UP-ARROW', 'DOWN-ARROW'



**** Zoom Mode ****

Keystroke Description

'MS-LEFT' To increase the size of the Zoom Box.
'MS-RIGHT' To decrease the size of the Zoom Box.
The size of the Zoom Box is determined as a percentage
of the currently displayed region. By default both axis
use the same percentage, however by holding down the 'h'
'v' key while clicking the left or right mouse button
one axis may be expanded or contracted independent of
the other.
'^H' To set the Horizontal Zoom Box to the Full Displayed region.
'^V' To set the Vertical Zoom Box to the Full Displayed region.
'MS-MIDDLE' To expand the region within the Zoom Box and return to
previous mode, e.g. Peak-Pick Mode. A quick way to zoom
in on the current cursor location is to click on the
Middle mouse Button twice.
'ESC' To escape from the Zoom Mode without expanding the Zoom Box.
PIPP returns to the previous mode, e.g. Peak-Pick Mode.
You can also escape the Zoom Mode by slowly moving the
cursor outside the contour plot region.


**** Jump Mode ****

Keystroke Description

'0' - '9' To enter the new slice number or chemical shift or residue
number or spin-system ID. As the keys are pressed they
will be echoed in the Status Window next to the prompt.
Input is assumed to be a slice number if the number is
an integer, e.g. no '.', and neithor the diamond key nor
a single letter residue code was entered. Input is
assumed to be a chemical shift if there is a '.' and/or
'p' or 'h' are entered after the number. Input is
assumed to be a residue number if the diamond/Alt modifier
key was used and/or the integer is preceeded by its
single letter amino acid code, e.g. "K31". Input is
assumed to be a spin-system if the integer is preceeded
by an ASCII character that is NOT a valid single letter
amino acid code, e.g. "#31".
'`' To Jump by Peak-ID number. This requires that a peak-pick table
has been created and read into pipp. Example `120 to jump
to the plane that has peak ID 120. Use DMD-L to put up
Cross Hairs so that the peak can be quickly found.
This is the backquote character usually found next to the '1'
key at the upper left of the keyboard. If you can not find
find the backquote the backslash '\' will also work.
'.' To enter a floating point number which gets interpreted as
a chemical shift in PPM. Note the PPM is folded into the
spectrum if the value entered is outside the sweep width.
'p' To enter a PPM chemical shift without entering a '.'. Note
the 'p' should be the last character entered.
'h' To enter a Hz chemical shift. The '.' is optional. Note the
'h' should be the last character entered.
'DELETE' To Edit the entered slice number. Will not work after a
'p' or an 'h' has been entered.
'RETURN' To go to the desired slice and return to previous Input mode.
'MS-LEFT' To go to Slice specified by clicking 'MS-LEFT' over a
perpindicular trace, e.g. to a specific Z plane.
This will only work if a perpindicular trace is displayed.
'ESC' To escape from the Jump Mode without going to a new slice.


**** Look-Only Mode ****

Keystroke Description

'ESC' To Exit/Escape from Look Only Mode. The NMR data slices
'e' appropriate to the current slice will be read in and
Peak-Pick Mode will be resumed.
'c' To Toggle display of the Contours on/off.

Look Only Commands that are the same as in the Peak-Pick Mode.

'MS-MIDDLE', 'p', 't', 'SPACE', 'j', 'DOWN-ARROW', 'UP-ARROW', 'RIGHT-ARROW',
'LEFT-ARROW', 'o', 'g', 'f', 'd', 'u', 'i', '2'


**** 2-Contour Mode ****

Keystroke Description

'ESC' 'e' To Escape/Exit from 2-Contour Mode.
'1' To Toggle Display of the first Contour Plane on/off.
If Exp has symmetry and it is required then this
plane will show the peak that was clicked on in Inform
peak Mode and show box to the symmetry peak with a smaller
box the size of the error range that was used.
'2' To Toggle Display of the second Contour Plane on/off.
'SPACE' To Toggle which plane is on top. Note color changes and
which slice number is printed in the top border. The 'j'
and 'p' commands operate only on the top plane.

2-Contour Commands that are the same as in the Peak Pick Mode.

'MS-MIDDLE', 'j', 't', 'p', 'f', 'd', 'u', 'o', 'g', 'DOWN-ARROW',
'UP-ARROW', 'RIGHT-ARROW', 'LEFT-ARROW'


**** Contour Level Setting Mode ****

Keystroke Description

'ESC' To Escape from Contour Level Setting Mode without
changing levels.
'e' To exit from Contour level setting mode at the new level.
'm' To set level Multiplier. Prompts for floating point input.
't' To set minimum absolute Threshold. Also prompts for float
input. After the return has been hit upon entering the
input for the 'm' or 't' command the contours will be
re-calculated.
'l' To set minimum level of contours to be displayed.
This is very fast since the contours are NOT re-calculated.

Contour Level Setting Commands that are the same as in the Peak
Pick Mode.

'MS-MIDDLE', 'SPACE', 'p', 'o', 'g', 'f', 'd', 'u'


**** Plane Trace Mode ****

Keystroke Description

'ESC' 'e' To Escape/Exit from Plane Trace mode.
'MS-LEFT' To Jump/Drag the Trace Position. This is how different traces
along the same axis are selected. By holding down on
the 'MS-LEFT' key the Trace Positon is dragged. The
border for the Contour Window shows which trace is
currently displayed.
'MS-RIGHT' To adjust the intensity or the Offset of the trace.
To Adjust the trace intensity, position the mouse within
the box enclosing the 2D plot near a trace point and
then while holding down on the 'MS-RIGHT' key move the
mouse away or towards the zero intensity line to
increase or decrease the trace intensity.
To Adjust the Trace Offset, position the mouse OUTSIDE the
box containing the 2D plot and then after depressing
and holding the 'MS-RIGHT' key move the mouse in the
direction that you want the trace to move. Note
however, that a trace displayed horizontally can only
be moved vertically and a trace displayed vertically
can only be moved horizontally.
'p' To initiate Phase Adjust of 1D Trace. Note this performs a
Hilbert Transform (ie original data MUST be real only).
'c' To toggle display of contours on or off.
'SPACE' To toggle display of trace on or off. Only the display of the
trace is toggled, PIPP is still in the Plane Trace Mode.

Plane Trace Commands that are the same as in the Peak Pick Mode.

'MS-MIDDLE', 'g', 'f', 'd', 'u', 'j', 'DOWN-ARROW', 'UP-ARROW', 'LEFT-ARROW'
'RIGHT-ARROW'


**** Perp. Trace Mode ****

Keystroke Description

'ESC' 'e' To Escape/Exit from Perp. Trace mode.
Note all selected traces will be remebered next time trace
mode is entered.
'DEL' Delete Key to delete all Perp. Traces so that new traces may be
selected. Individual traces may be deleted using
'MS-LEFT' on the peak for the active trace.
Delete Key is actually a toggle between current set of
traces being selected and NO traces being selected.
'MS-LEFT' To Select/Unselect a trace at a nearby data point that is a
local maximum. One of three operations described below
the the 'CRTL-MS-LEFT' command will be performed on
this point.
'CRTL-MS-LEFT' To Select/Unselect a trace at the nearest data point, ie does
NOT look for a nearby local maximum. For 'MS-LEFT' and
'CRTL-MS-LEFT' one of three operations will be perfomed
depending on whether this trace is the active trace.
(1) If this point corresponds to the active trace it will
be unselected and undisplayed.
(2) If this point does not correspond to the active
trace but does correspond to a previously selected
trace that is still in memory then this trace will
be the active trace. The previous active trace is
kept in memory and can selected at a later time.
(3) If this point does NOT correspond to a trace that has
been selected then the data points for this trace will
be read in unless all of the trace buffer locations
have been filled up. This takes between 1 to 5
seconds as one point from every slice must be read.
'MS-RIGHT' To adjust the intensity or the Offset of the trace.
Note this is EXACTLY the same as was used for Plane
Trace Mode.
'p' To initiate Phase Adjust of 1D Trace. Note this performs a
Hilbert Transform (ie original data MUST be real only).
'c' To toggle display of 2D contours on or off.
'SPACE' To toggle trace display on or off. Only the display is toggled
PIPP is still in the Perp. Trace Mode.
'j' To jump to a new slice. Note that during the jump the 'MS-LEFT'
key may be used to select a slice from the trace.

Perp. Trace Commands that are the same as in the Peak Pick Mode.

'MS-MIDDLE', 'g', 'f', 'd', 'u', 'o', 'DOWN-ARROW', 'UP-ARROW', 'LEFT-ARROW'
'RIGHT-ARROW'


**** Phase Adjust 1D Trace Mode ****

Keystroke Description

'ESC' 'e' To Escape/Exit from Phase Adjust 1D Trace mode.
Note current phase and pivot values will be remembered
(ie can exit mode select new trace and last used
PC0, PC1 values will automatically be applied).
New phase will NOT be applied to the data set, must
use nmrPipe or another processing software.
'MS-LEFT' To vary interactively PC0, PC1 or Pivot Point. The commands
'0', '1', 'b', 'p' select which phase params gets varied.
For instance after hitting '1' PC1 will be changed by
dragging the Left Mouse button. The '1' key must NOT
be held during the drag. The status window indicates
which param is getting varied and the current phase
values are shown in the title of the Contour window.
'MS-RIGHT' To adjust the intensity or the Offset of the trace.
Note this is EXACTLY the same as was used for Plane
Trace Mode.
'0' To set Left Mouse Button to adjust PC0. (this is number zero)
This is default mode upon entering Phase Adjust 1D trace.
If current mode is Adjust PC0 then this will toggle to
whatever phase mode was previous.
'1' To set Left Mouse Button to adjust PC1.
'b' To set Left Mouse Button to adjust both PC0 and PC1.
PC0 is restrained to -0.5 * PC1
'p' To set Left Mouse Button to adjust Pivot Point.
Default Pivot point is 0 and is NOT shown.
's' To set Left Mouse Button to Scroll Trace Position.
This lets you change traces and will automatically
perform the Hilbert Transform and phase each trace.
'm' To set Pivot Point to center of acquired spectrum.
Assumes center is (0.5 * Size) + 1
'r' To display the real (ie absorptive signal).
'i' To display the imaginary (ie dispursive signal).
'x' To toggle between displaying real or imaginary.
't' To type in desired PC0 and PC1 values.
'c' To toggle display of 2D contours on or off.
'SPACE' To toggle trace display on or off. Only the display is toggled
pipp is still in the ZA trace mode.
'j' To jump to a new slice. Note that during the jump the 'MS-LEFT'
key may be used to select a slice from a perp. trace.

Phase Adjust 1D Trace Commands that are the same as
in the Peak Pick Mode.

'MS-MIDDLE', 'g', 'f', 'd', 'u'


Program initialation can be controlled by a set of environment variables
listed below. However, default values will be used for environment variables
that are not set. To set environment variables use the unix command:
setenv <Environment-Variable> <Value of Variable>
Always use the same variable type as shown in the default, ie integer, real
or string. Also, if the Variable requires several strings separated by
spaces then it should be enclosed in double quotes.

Since many of the environment variables described in ps_contour.help,
contour_sim.help and capp.help are also utilized in pipp.c only the differences
between the previous programs and pipp.c environment variables are listed
below. Refer to the previous help files for more information.


Environment Default Purpose of Variable
Variable Value


*** Byte-Swap Variables *** Controls Byte-swapping of data
Floating point and integer representation differs between PC's
running Linux and Unix (ie Sun and SGi). Both float and int are
4 bytes in length. Only non-ASCII files such as NMR data,
*.XTRMA and *.CNTR files need to be byte-swapped when the
data was recorded under Linux and viewed under Unix.
The byte swapping is: ABCD <--> DCBA

DIAG_BYTE_SWAP 0 When set to non-zero show byte-swap diagnostics.
This will let you know whether byte-swapping
is taking place or not for each file.
BYTE_SWAP_AUTO 1 When possible automatically sense if byte-swapping
should be performed. Note NMRi data can NOT
automatically be sensed for byte-swapping.
BYTE_SWAP_RD_ACQ, BYTE_SWAP_RD_CNTR and
BYTE_SWAP_RD_XTRMA take precedence, ie
overide this, if they are set.
BYTE_SWAP_RD_ACQ - When set to non-zero force byte-swapping to
take place when reading processed NMR data.
If explicitly set to 0 then byte-swapping will
NOT occur when reading processed NMR data.
When BYTE_SWAP_RD_ACQ is not explicitly set
and auto-sense is enabled then byte-swapping
is determined when the header params are
read from the first plane only, ie byte-swapping
is NOT determined on a plane by plane basis.
BYTE_SWAP_RD_CNTR - When set to non-zero force byte-swapping to
take place when reading contour files.
If explicitly set to 0 then byte-swapping will
NOT occur when reading contour files. When
BYTE_SWAP_RD_CNTR is not explicitly set and
auto-sense is enabled then byte-swapping
is determined for each 2D contour plane by
counting the number of tokens which mark
the end of each contour list for both non-swapped
and swapped contour data.
BYTE_SWAP_RD_XTRMA - When set to non-zero force byte-swapping to
take place when reading extrema files.
If explicitly set to 0 then byte-swapping will
NOT occur when reading extrema files. When
BYTE_SWAP_RD_XTRMA is not explicitly set and
auto-sense is enabled then byte-swapping
is determined when the extrema file is read in.



*** Chart Variables *** Controls position, orientation and look of plot.

LOOK_ONLY 0 Starts pipp in Look-Only Input Mode, but you can
use 'ESC' to exit. If first slice is not
contoured then program will exit.
APPEND_FILE Not available in pipp.c
PAGE_OUT Not available in pipp.c
SPLIT_X Not available in pipp.c
SPLIT_Y Not available in pipp.c
OVERLAP_X Not available in pipp.c
OVERLAP_Y Not available in pipp.c

PLOT_ALL_SLICES 1 Not available in pipp.c
Other Chart Variables same as desciption in ps_contour.help,
contour_sim.help and capp.help


**** Spectral Expansion Variables ****

SLICE_END_Z Not available in pipp.c
Other Spectral Expansion Variables same as desciption in ps_contour.help


**** Z and A Acquisition Variables ****

AXIS_ON_PLANE "X_AXIS Y_AXIS" Which two axis are used to define the plane.
This decides what plane is contoured and displayed.
For 3D data can choose X_AXIS Z_AXIS and also
Y_AXIS Z_AXIS. This create a new subdirectory
using the basename with the extension
.XZ or .YZ. If DATA_GROUPED is SINGLE_DATA_FILE
then the name of contour subdirectory for XY
will also have the extension .XY.
DATA_HEADER_SZ 2048 Number of bytes in header.
DATA_GROUPED 2D_FLS Specifies the arrangement of NMR data. Options
are: 2D_FLS 3D_FLS 4D_FLS SINGLE_DATA_FILE.
The Zant format is similar to SINGLE_DATA_FILE,
but has not been tested, ie may be slight
differences in header parameters.

No changes from description in contour_sim.help and capp.help


**** Ellipse Fitting Variables ****

Ellipse Fitting not available in PIPP, variables have no effect.


**** Simplex Optimization Variables ****

Simplex Optimization not available in PIPP, variables have no effect.


**** Peak Definition Variables ****

USE_EXTREMA 1 If non-zero will calculate and use an extrema file.
Extrema are calculated only once and then
stored on disk. Extrema are required for 3D
symmetry and Strip Manipulation.
PK_FILE_NAME - File name for peak pick file table.
Should be same as used in capp.
Defaults to base name for 3D data files,
ie "HNCA"
XVW_DSPLY_CTL 0 If this is set to 1 then the contours which were used
to define the peak center using Contour Peak-Picking
will be highlighted in a different color. Note
in order to use '^F' in PIPP this must be set to 1.
XVW_AUTO_SEL_ASSIGN 0 If set to 1 then in "Name Peak-Pick Mode" if there is
only one assignment given the constraints it will
be automatically selected and assigned. If this
is set to 0 then user will have to manually
enter the single choice (or enter escape).
ELL_PERC_MIDL_USE 100.0 If this is set by user or if PK_USE_PARAB_XY is
set to 0 then PIPP will start in Contour
Peak-Pick Mode and XY peak positions will be
determined by the average of the center of
selected contours. The parameters
ELL_PERC_MIDL_USE and ELL_FRACT_MIDL_LVL dictate
what contours are selected. Also, the display
shows which contours are selected by having
the selected contours displayed in a different
color then they should be, ie selected positive
contours are displayed with the color of
negative peaks.
ELL_FRACT_MIDL_LVL 0.5 Sets the fraction of peak intensity at which to
take the contours to define peak position. The
interactive command '^F' adjusts this.
XVW_PK_TBL_SZ 30000 Size in bytes of Peak Table Buffer. If you have
a very large number of peaks on a SINGLE
plane this will have to be increased. Current
should be large enough for around 500 peaks.
XVW_DSPLY_PK_TABLE 1 Flag to indicate whether the Peak-Pick Table should
be displayed when PIPP begins. The default
will have the Table displayed. Set to 0 to
not have the Table displayed. Note the command
't' will interactively toggle this flag.
XVW_PK_UNFOLD_X - Determines how display of possible unfolded shift
XVW_PK_UNFOLD_Y values is determined for each axis.
XVW_PK_UNFOLD_Z If folding is allowed the default value is:
XVW_PK_UNFOLD_A "-1 1" which displays an unfolded value -1*SW
and +1*SW for axis in which folding in is
defined in the stapp_exp.par file.
NOTE this has NO effect on how or whether PIPP
can find an assignment for a given peak. This
is only used in "Inform Peak" and "Name Peak"
mode to display in parenthesis possible unfold
values.
INTERP_INTENS 0 If non-zero will calculate Intensity using a 3 point
parabolic interpolation. If 0 then reports the
intensity from the local extrema, ie tallest point.
For most data this makes no difference at all, ie
reported intensity is unchanged by interpolating.
This can be interactively toggled using ^I in pipp.
PK_TABLE_FORMAT 0 Set to 1 to read in a .PCK file.
Default will read in a .ASG file.
Sorry about the similiarity between this Variable
and PK_TBL_FRMT. When All info comes from
parameter files I will try to better differentiate.
PK_TBL_FRMT "%7.2f" Format for Peak Table Columns. To specify a seperate
format for each axis use double quotes as in:
"%8.3f %8.3f %6.1f". Note this is same as in capp
INTENS_PCK_FRMT " %+8.2e" Format for .PCK Peak Pick Table Intensity
This will also adjust the Intesity format for
the Inform Mode in pipp.
INTENS_ASG_FRMT "%8.2e" Format for .ASG Peak Pick Table Intensity
INTENS_PIPP_FRMT "%6.1e" Format for Interactive Peak Pick Table Intensity
ASSIGN_PCK_FRMT "%-25s" Format for Assignment string for .PCK file.
This is also used in CAPP and STAPP.
XVW_LBL_FRMT 0 Format for writing Peak Label in pipp.
This only affects display in X11 window.
To change plotted output use PS_LBL_FRMT
0 => ID; 1 => String; 2 => Assignment;
3 => ID and String; 4 => ID and Assignment
PK_WR_ASSIGN 0 If non zero then Assignments are written with
the Peak Table.
XVW_MAX_PK_XSAME 0.5*dRes_X Interactive peak editting width along X.
XVW_MAX_PK_YSAME 0.5*dRes_Y Interactive peak editting width along Y.
XVW_MAX_PK_ZSAME 0.5*dRes_Z Interactive peak editting width along Z.
XVW_MAX_PK_ASAME 0.5*dRes_A Interactive peak editting width along A.
Can not add peaks using interpolation
closer than specified by these values.
Other Peak Definition Variables same as description in contour_sim.help


**** Ridge Definition Variables ****

Ridge Definition not available in PIPP, variables have no effect.


**** Enabling 3D Symmetry without Assignments ****

SYM_AXIS - Two Axis which get swapped when symmetry is performed.
Use two from: X_AXIS Y_AXIS Z_AXIS A_AXIS
Enclose both axis in double quotes as in:
"X_AXIS Y_AXIS"
Default value is to not do symmetry UNLESS
a stapp.par is defined with an Exp that
has symmetry. Using a stapp.par will
enable pipp to unfold shifts that may be
folded in.
SYM_ERROR - Error to use for locating Symmetry Peaks (in PPM).
Only use one value which is used for both axis.
Default is average digital resolution.
Can be interactively changed in Inform Mode
with '^E' command.


**** StriP Variables ****

SM_MIN_LENGTH 6 Minimum Number of Strips to display.
SP_PER_PAGE - Number of Strips to display on screen.
Defaults to all Strips.
SP_SEQ_ORDER_FL If set then this file is opened and defines the
Manipulated Order for the Strips. The Manipulated
Order can be displayed by hitting a '2'. There are
2 keywords that are used in SP_SEQ_ORDER_FILE:
SP_SEQ_ORDER A list of integers which gives
the Manipulated Order. Blanks
are inserted using -9999
This keyword must be in the file.
SP_SEQ_ASSIGNED A single integer which gives the
Residue Number for the first
Strip. If absent then the
re-ordered strips are unassigned.
STAPP_PAR_FL - A parameter file used with stapp program but has
several Variables which are used in pipp.
See also the stapp.help file.
The following Variables are used in pipp:
EXP_NAME, NON_SP_PAR, XPLR_FILE_NAME,
MAX_NOE_DIST, PDB_ATM_NM_FILTER, PDB_FILES,
DIM_COUNT, THRESHOLD, ACQ_BASE_PHASE,
ANTIPHASE_FOLDOVER, SHIFT_TBL_TYPE,
DATA_OFFSET, ERROR_RANGE, DEG_PROX_LIMIT,
SEQUENCE, SYM_ERROR, DEG_INTENS_FCTR,
NOE_KEAP_INTRA, DIST_FROM, REQ_ND_SYM,
PROG_PATH, AA_PAR_FL, EXP_PAR_FL
The EXP_NAME is the name of the experiment and a
key into the STAPP_EXP_FL which contains
defintions about every NMR experiment stapp or
pipp will use.
Other Strip Variables Definitions same as in ps_contour.



**** Interactive Window Variables ****

STD_OUT_CMND "\0" Can be set to any text string. This string is
sent to stdout when the user is in Std Out
Peak Mode and clicks the Left Mouse button
over a peak. This is intended to be a command
that is interpreted by a shell script such as
tcl. This is very primitive and there are no
publicly available scripts that use this feature.
WNDW_DRAW_PK_LBL_BOX 1 If set to 1 will draw a box around the Peak Label.
If 0 will not draw box around peak label.
This gets around a problem with Solaris 2
with X11 R5 that incorrectly draws the box
around the peak when showing the Peak Label.
PK_FONT_SIZE 10 Font point size used for labelling peaks.
SCL_FONT_SIZE 10 Font point size used for labelling scale.
TXT_FONT_SIZE 10 Font point size used in text subwindow.
DEFAULT_THICK 0 Default Pixel Line thickness for drawing all lines.
A value of 0 means use the thinnest line and
the fasted drawing algorithm. Evan setting
DEFAULT_THICK to 1 will use a slower drawing
algorithm to get the corners connected "right".
CNTR_THICK 0 Pixel Line thickness for drawing contours.
GRID_THICK 0 Pixel Line thickness for drawing grid lines.
BORDER_THICK 0 Pixel Line thickness for drawing border lines.
TRACE_THICK 0 Pixel Line thickness for drawing traces.
FRACTION_X 0.7 Fraction of full page along X dimension.
FRACTION_Y 0.7 Fraction of full page along Y dimension.
WIN_CNTR_XW - Absolute width along X dimension.
WIN_CNTR_YW - Absolute width along X dimension.
WIN_CNTR_XW and WIN_CNTR_YW are calculated
from FRACTION_X and FRACTION_Y times
a standard 8 1/2" by 11" dimensions unless
the user sets their values explicitly.
Note the resize corners now work within pipp.
TEXT_BG "white" Color for Background to PIPP-STATUS windows.
TEXT_FG "black" Color for Foreground to PIPP-STATUS windows.
BACK_COLOR "black" Background Color for Contour Window.
POS1_COLOR "wheat" Color for Positive Contours.
NEG1_COLOR "magenta" Color for Negative Contours.
POS2_COLOR "GhostWhite" Color for X, Y, Z and A Trace line.
NEG2_COLOR "SlateBlue1" Color for Highlighting Z and A Trace Point which is in
|| common with the current 2D Slice.
----> See Xlib Reference Manual (Vol. 2 of series) p 589
for the names of the colors available in X. Or
the names can be found in /usr/lib/X11/rgb.txt




Version 4.3.2 ( 03/15/00 )


more /S1/Apps/Dan/bin/pipp.help