Using PROG_PATH /S1/Apps/Dan/bin
/s/Apps/DanBin/ps_contour.sgi5 help
Documentation: ps_contour.help Program: ps_contour.c
Date Editted: June, 1997 Purpose: 2D NMR Contouring
By: Dan Garrett


Program requires a minimum of three arguments:

ps_contour <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 contour plot
are controlled through shell environment variables described below.

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

Program output 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. X dimension will be F2 (Acq) if data from NMRi is not transposed.
The Z dimension corresponds to the third dimension.

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.

PLOT_CONTOURS 1 Plot contours if non-zero. For 3D and 4D data this
may be set to 0 in order to quickly create the
binary contour files for use in pipp without
creating or plotting a PostScript file. A single
file, POSTSCRIPT, is re-used as an intermediary
to the plot. Therefore do NOT run two copies of
ps_contour that are generating plots in the same
directory at the same time.
LOOK_ONLY 0 If non-zero then the NMR data matrix will NOT be
read in. The NMR data MUST already be contoured
or the program will generate an error message and
exit. This can save considerable time when
dealing with large datasets that have already been
contoured. The only time LOOK_ONLY must be 0 is
during Contour generation.
PLOT_FILE POSTCRIPT Name of file used to write Postcript file that is sent
to printer. If more than one program is creating
and plotting data than different files should be
used for each program.
PLOT_COM lpr Spooling command to use for sending PostScript plots to
printer. Should be lpr on a sun computer using BSD
or lp on an sgi computer using system V. If the
Environment Variable BINTYPE is set to sgi then
will default to lp. The sgi OS has the option of
installing the lpr spooling daemon to print to remote
printers on a sun computers. In addition if
you are running SunOS 5.x then you are using
the System V OS and are probably spooling with lp.
Which means BINTYPE alone can NOT determine how
program should print, you must find out how you
spool PostScript files to your printer and set
PLOT_COM accordingly. If PLOT_COM is explicitly
set to lpr or lp then the three parameters,
PRINT_COM, PLOT_CALL and PLOT_OPT, will assume a
default value consistent with PLOT_COM instead
of BINTYPE.
PRINT_COM lpr Spooling Command to use for printing text files such as
lpr, lp, enscript or your favorite text to
PostScript conversion program. For BINTYPE sgi lp
is the default. If PLOT_COM is explicitly set then
PRINT_COM will default to what was used for PLOT_COM
independent of BINTYPE.
PLOT_CALL -P Arguement flag for calling printer which is -P on
BSD (sun) and -d on System V (sgi) computers.
If BINTYPE is set to sgi than will default to -d.
If PLOT_COM is set to lpr than will default to
-P independent of BINTYPE. If PLOT_COM is set to
lp then will default to -d independent of BINTYPE.
PLOT_OPT -h Any Options to submit with the Spool command. If
BINTYPE is sgi the PLOT_OPT will default to "".
This can be used to send any desired options.
PRINTER lp Printer to which POSTSCRIPT plot file will be sent.
PAPER_SIZE REGULAR Paper size is Regular 8 1/2 by 11 inch.
Use LEDGER to set 11 X 17 paper and automatically
set correct margins and paper tray.
New Defaults when PAPER_SIZE is set to LEDGER are:
PAPER_TRAY 1; TOP_MARGIN 2.2;
BOTTOM_MARGIN 2.0; LEFT_MARGIN 1.6;
RIGHT_MARGIN 2.5; PAPER_XW 27.94;
PAPER_YW 43.18
These defaults can be overriden by explicitly
entering values for the environment variables.
PAPER_TRAY 0 Which Paper Tray to use. On Data Products LZR 1560
Tray 0 is Top Tray and Tray 1 is Bottom Tray. On
LZR-1560 type printers. Use -1 to NOT select
any Tray, ie will not issue PostScript command for
selecting Tray. When setting up an LZR-1560 make
sure that the 11x17 paper tray is on the BOTTOM.
If 3 trays are used then 11x17 should be the
middle tray. If this is done then the single
variable PAPER_SIZE will correctly select the
desired paper tray.
PS_TRAY_COMMAND * PostScript command to select alternative tray
for Ledger size paper. Default is string:
"statusdict begin 1 setpapertray end\n"
which is appropriate for DataProducts printer.
For HP4MV or HP4V use string:
"%%%%BeginFeature: *PageSize Tabloid\n <</DeferredMediaSelection true /PageSize [792 1224] /ImagingBBox null>>\n setpagedevice\n%%%%EndFeature\n"
Check with printer manufacturer for other
postscript printers.
PS_HEADER_COMMAND - Arbitrary string to include in header of
PostScript output. NOTE this MUST be a
valid postscript command otherwise the
printer may not produce any output.
NEGATIVE_ONLY 0 Plot only negative contours if value is non-zero
POSITIVE_ONLY 0 Plot only positive contours if value is non-zero
If both are non-zero then positive and negative
contours are plotted as if they were both zero.
MAX_LVLS 64 Maximum number of positive or negative contours.
If Set to 0 will get NO contours. If set to 1
will get 1 positive and 1 negative contour.
If binary contours are being created this may
limit the number of contours observed during later
viewings of this slice.
MAX_POS_LVLS MAX_LVLS Maximum number of positive contours.
MAX_NEG_LVLS MAX_LVLS Maximum number of negative contours.
SLEEP_TIME 30 Time to wait (in Sec) between multiple plots.
This is not only courteous but necessary if you are
plotting large files. Large files (~ 1 MgByte) use
a large amount disk space that the system disk
also uses for swap space. That means if you queue
up too many large plots NO one will be ably to do
anything on the computor with that printer queue.
VIEW_IN_PORTRAIT 1 Plot drawn to be viewed in portrait if non-zero.
Otherwise plot is drawn in Landscape.
SWITCH_XY_AXIS 0 X and Y axis switched if value is non-zero.
This does NOT change the NMR data, this only
changes how the data is displayed.
See plot orientation diagrams below for description
of effect of VIEW_IN_PORTRAIT and SWITCH_XY_AXIS.
PK_FILE_NAME - Specifies name of Peak-Pick file to be read in and
used to annotate the Peaks. The variable
PK_TABLE_FORMAT determines whether a .ASG or a
.PCK file is read. Type of Annotation is
determined by selecting one of: MARK_OFFSET_ID,
MARK_ID and MARK_PEAKS. By default the Peaks are
NOT annotated.
PK_TABLE_FORMAT 0 To read in a .PCK format table set this to 1.
Otherwise a .ASG format table is read in.
MARK_OFFSET_ID 0 If not 0 will annotate peaks with a box around each
peak and the Peak ID number displayed Offset
from the center of the peak, ie not on peak.
MARK_OFFSET_ID takes precedence over MARK_ID and
MARK_PEAKS.
MARK_ID 0 If not 0 will annotate peaks with Peak ID number
centered on top of the Peak. MARK_ID takes
precedence over MARK_PEAKS.
MARK_PEAKS 0 If not 0 will annotate peaks by putting a box around
each peak. No ID number is printed. I am not
sure why I keap this option around?
PS_LBL_FRMT 0 Format for writing Peak Label in ps_contour.
0 => ID; 1 => String; 2 => Assignment;
3 => ID and String; 4 => ID and Assignment
CNTR_IGNR_BIN_FL 0 Ignore any existing binary contour file if non-zero.
If no binary file exists none will be created, and
if one exists it will be ignored. Set this flag
to 1 if you plan on changing the threshold and
do not want to remove the .CNTR file.
CNTR_RPLC_BIN_FL 0 Replace any existing binary contour file if non-zero.
The program will automatically create a sub-
directory with the same name as the base name
for the 3D or 4D file set and create a binary
file of the contours as each slice is processed.
These two flags control the behavior of the
program with respect to binary contour files.
Once the binary files are created they are used
by default unless you use one of these flags or
delete the files with the Unix command "rm".
If the Abs. Threshold or the level multiplier is,
changed or the spectral width is increased the
program will give an Error message which
indicates that the desired contours can NOT be
obtained from the binary files.
APPEND_FILE 0 Current plot appended to the file POSTSCRIPT if not 0
Otherwise the POSTSCRIPT file is written over.
PAGE_OUT 1 Current plot is last before page written if not 0
Otherwise more plots are expected on this page.
APPEND_FILE and PAGE_OUT are used for creating
a single postscript file (all on one page) that
has several 2D plots.
PS_MACRO_FILE - Name of file which contains user defined PostScript
macros to be included in the postscript file.
The text in PS_MACRO_FILE must be valid postscript
commands otherwise the printer may not produce
any output, ie no plot. There is no default file,
but there is a file called annot_macros.pps in
the PIPP bin directory that is an example.
This example has a set of annotation macros
for PostScript output.
PS_ANNOT_FILE - Name of file which contains user defined PostScript
annotation commands which are included at the
end of the PostScript file. The text in
PS_ANNOT_FILE must be valid postscript commands
otherwise the printer may not produce any output,
ie no plot. There is no default file, but
there is a file called annot_commands.pps in
the PIPP bin directory that is an example.
This example has a set of annotation commands
which require annot_macros.pps for adding
annotation to the PostScript output.
LEFT_MARGIN 1.0 Left margin to plot in cm.
RIGHT_MARGIN 2.0 Right margin to plot in cm.
TOP_MARGIN 1.5 Top margin to plot in cm.
BOTTOM_MARGIN 1.5 Bottom margin to plot in cm.
The *_MARGIN variables control how big and where
the plot will appear on the page. The orientation
that is desired determines which edge of the plot
is top. TOP_MARGIN is always the top of the plot
page.
CNTR_LIN_LEV 0 Construct Contours using Contour Multiplier as a Linear
Level Offset if not 0 instead of a multiplier.
For instance if Threshold is 10.0 and "Multiplier"
is 0.5 then the levels will be 10.0, 10.5, 11.0,
SPLIT_X 1 Number of pages to use in plotting spectrum along
NMR X axis. Note default is 1, ie use 1 page
for X axis. Any non-negative number may be used.
SPLIT_Y 1 Number of pages to use in plotting spectrum along
NMR Y axis. Note default is 1, ie use 1 page
for Y axis. Any non-negative number may be used.
OVERLAP_X 500.0 Overlap (Hz) between split plots along X axis.
OVERLAP_Y 500.0 Overlap (Hz) between split plots along Y axis.
Spectrum will appear expanded on seperate pages.
PLOT_X_EDGE 1 Edge along X drawn if value is non-zero.
PLOT_Y_EDGE 1 Edge along Y drawn if value is non-zero.
PLOT_FILE_NAME 1 File name written on plot if value is non-zero.
Setting to 0 will also turn off printing of
PLOT_COMMENT.
PLOT_COMMENT '\0' Any Text that will be written in upper right corner
above the plot. String < 64 chars.
Default is no comment.
PLOT_X_SCALE 1 Scale along X drawn if value is non-zero.
PLOT_Y_SCALE 1 Scale along Y drawn if value is non-zero.
PLOT_X_GRID 1 Grid along X drawn if value is non-zero.
PLOT_Y_GRID 1 Grid along Y drawn if value is non-zero.
XGRID_ON_DP 0 Grid along X set to data values if non-zero.
YGRID_ON_DP 0 Grid along Y set to data values if non-zero.
XGRID_ON_DP and YGRID_ON_DP are primarily useful
for debugging some aspects of the program.
GPC_X 2.0 Max. # of grid lines per cm along X.
GPC_Y 2.0 Max. # of grid lines per cm along Y.
Grid lines are computed from GPC_X & GPC_Y unless
XGRID_ON_DP or YGRID_ON_DP are set.
TPC_X 2.0 Max. # of tic lines per cm along X.
TPC_Y 2.0 Max. # of tic lines per cm along Y.
X_UNITS PPM Units for X output. Allows PPM Hz PTS.
Y_UNITS PPM Units for Y output. Allows PPM Hz PTS.
Z_UNITS PPM Units for Z output. Allows PPM Hz PTS.
A_UNITS PPM Units for A output. Allows PPM Hz PTS.
PAPER_XW 21.59 Width of plot output in cm. (8 1/2 ")
PAPER_YW 27.94 Heigth of plot output in cm. (11")
Do not change PAPER_XW or PAPER_YW unless plotter
page is not a standard 8 1/2 by 11 inch paper.
See VIEW_IN_PORTRAIT and SWITCH_XY_AXIS for
changing plotter output orientation. Note 11x17
inch paper is selected using PAPER_SIZE "LEDGER"
SCALE_BOTTOM 1 Plot scale along Bottom edge if value non-zero.
SCALE_RIGHT 1 Plot scale along Right edge if value non-zero.
CNTR_THICK 0.01 Thickness of Contour Lines. For Publications try
0.6 and then optimize for appearance.
PS_FONT "Times-Roman" Font for ALL text output. See pages 260-267 of
the PostScript Language Reference Manual for
a "standard" set of fonts. Case Sensitivity
varies with the printer so be carefull.
FONT_SIZE 12.0 Point size used for Scale. For Publications try
16.0 and then optimize for appearance.
PK_FONT_SIZE 8.0 Point size used for Peak Label. For Publications try
16.0 and then optimize for appearance.
PS_BGC_RED - Red component to BackGround Color, varies 0.0 -> 1.0.
PS_BGC_GREEN - Green component to BackGround Color, varies 0.0 -> 1.0.
PS_BGC_BLUE - Blue component to BackGround Color, varies 0.0 -> 1.0.
By default the *_BGC_* are not used, ie
output is black and white only
0.0 is no contribution and 1.0 is full.
PS_POS_RED - Red component to POSitive Contours, varies 0.0 -> 1.0.
PS_POS_GREEN - Green component to POS. Contours, varies 0.0 -> 1.0.
PS_POS_BLUE - Blue component to POS. Contours, varies 0.0 -> 1.0.
By default the *_POS_* are NOT used, ie
output is black and white only
0.0 is no contribution and 1.0 is full.
PS_NEG_RED - Red component to NEGative Contours, varies 0.0 -> 1.0.
PS_NEG_GREEN - Green component to NEG. Contours, varies 0.0 -> 1.0.
PS_NEG_BLUE - Blue component to NEG. Contours, varies 0.0 -> 1.0.
By default the *_NEG_* are NOT used, ie
output is black and white only
0.0 is no contribution and 1.0 is full.
PS_ANN_RED - Red component to text ANNotation, varies 0.0 -> 1.0.
PS_ANN_GREEN - Green component to text ANNotation, varies 0.0 -> 1.0.
PS_ANN_BLUE - Blue component to text ANNotation, varies 0.0 -> 1.0.
By default the *_ANN_* are NOT used, ie
output is black and white only
0.0 is no contribution and 1.0 is full.
PS_SCL_RED - Red component to text SCaLe, varies 0.0 -> 1.0.
PS_SCL_GREEN - Green component to text SCaLe, varies 0.0 -> 1.0.
PS_SCL_BLUE - Blue component to text SCaLe, varies 0.0 -> 1.0.
By default the *_SCL_* are NOT used, ie
output is black and white only
0.0 is no contribution and 1.0 is full.
PS_GRD_RED - Red component to GRiD lines, varies 0.0 -> 1.0.
PS_GRD_GREEN - Green component to GRiD lines, varies 0.0 -> 1.0.
PS_GRD_BLUE - Blue component to GRiD lines, varies 0.0 -> 1.0.
By default the *_GRD_* are NOT used, ie
output is black and white only
0.0 is no contribution and 1.0 is full.
GRID_GRAY 0.1 Fraction gray for grid drawing grids.
CNTR_GRAY 0.0 Fraction gray for grid drawing contours.
SCL_GRAY 0.0 Fraction gray for grid drawing scale.
ANN_GRAY 0.0 Fraction gray for grid drawing annotations.
Fraction Gray: 0.0 for Black and 1.0 for White.
GRID_PATTERN "1 3" Postscript setdash dash pattern for Grid.
NEG_PATTERN "1.5 0.75" Dash pattern for negative Contours.
Postscript dash pattern first value is length of
black drawn and second is length of white space
drawn in units 1/72 inches. In order to draw
Negative Contours solid use the pattern ""
If NEGATIVE_ONLY is set then a solid line is
used for the negative contours.
LBL_FRMT_X "%1.1f" Format used in outputing X Scale lables.
LBL_FRMT_Y "%1.1f" Format used in outputing Y Scale lables.

**** Spectral Expansion 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.
HZ_START_X - Start of chemical shift along X (PPM).
HZ_START_Y - Start of chemical shift along Y (PPM).
HZ_END_X - End of chemical shift along X (PPM).
HZ_END_Y - End of chemical shift along Y (PPM).
PPM is assumed unless the shift is appended with
an h or an H ( no space between shift and h).
Default values are the entire 2D plane.
Command line arguments override these values.
SLICE_START_Z - Starting Slice number along Z for multiple plots.
SLICE_END_Z - Ending Slice number along Z for multiple plots.
SLICE_START_A - Starting Slice number along A for multiple plots.
SLICE_END_A - Ending Slice number along A for multiple plots.
Multiple slices will be plotted only if the
Z Acquisition variables have also been set.
If Z acquisition variables have been set then
SLICE_START_Z defaults to 1 and SLICE_END_Z to
Z_SLICES, ie plot entire 3D spectrum.
By Default A axis (4'th dimension) does not exist.
Setting A_SLICES to non-zero value requires all
A acquisition variables to be set.
Command line arguments override these values.


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

ACQ_PRM_FRMT NMRI2D Location and Format for Acquisition Parameters.
Valid options are: NMRI2D NMRI_PIPE
NMRI2D requires that Z and A acquisition
params be specified as Environment Variables
described below. NMRI_PIPE will read the
Z and A params from the NMRi like header
that was written by nmrPipe. NMRI_PIPE
requires that DIM_COUNT also be set.
If set to NMRI_PIPE then Z and A acquisition
Environment variables described below are IGNORED.
DIM_COUNT - Number of dimensions in the NMR data. Required.
Z_SLICES 0 Total number of data points along third dimension.
A_SLICES 0 Total number of data points along fourth dimension.
If *_SLICES is set to any non-zero value then all
of the Z or A Acquisition variables except
*_FLIPPED must be set unless ACQ_PRM_FRMT is
set to NMRI_PIPE.
Z_SF - Spectrometer Frequency (MHz) along Z axis.
A_SF - Spectrometer Frequency (MHz) along A axis.
Z_SW - Full Spectrometer Sweep Width (PPM) along Z.
A_SW - Full Spectrometer Sweep Width (PPM) along A.
Z_REFERENCE - Chemical Shift (PPM) of middle slice number along Z.
A_REFERENCE - Chemical Shift (PPM) of middle slice number along A.
For a 64 slice experiment the middle slice is 33.
Z_FLIPPED 0 Z-axis is upside down if non-zero.
A_FLIPPED 0 A-axis is upside down if non-zero.
This can happen if experiment was not set up
incorrectly so that the first slice corresponds to
the high field (low chemical shift) edge of
spectrum. In most cases *_FLIPPED should be 0.
Do NOT use this if ACQ_PRM_FRMT is set to
NMRI_PIPE. If Z or A should be flipped then
you MUST use Z_SLICES, Z_SF, Z_SW and
Z_REFERENCE to give reference or you MUST
use the REV function of nmrPipe and do not use
Z_FLIPPED. The problem is that the reference
information stored in the header for the data
is incorrect for any axis which should be
reversed, ie flipped, and there is no way
to easily determine the correct reference
parameters unless they are explicitly entered.

**** StriP (SP_) Variables ****
One axis is composed of strips or Planes
at a specific Pair of Frequencies, ie
at an N15, NH Frequency for a given Residue
for example 3D N15 NOESY into strips
or 4D N15, C13 into Planes
Must use program written by Stephan Grzesiek to create
the Strips or Planes.

SP_AXIS NO_AXIS Axis Along which StriPs are taken.
ie referencing for this axis is NOT
a chemical shift but an ID or Residue Number.
Other options: X_AXIS, Y_AXIS, Z_AXIS
SEQUENCE - Full amino acid sequence using single letter code.
Spaces are ignored. First amino acid in list
given residue # 1. Use \ at end of line to
continue sequence from one line to the next.
Double quotes around sequence also usefull.
This Variable is required evan if the protein
is unassigned, ie StriPs are not in Residue order.
SP_RES_START 1 First Residue to Display. If SP_AXIS is X_AXIS or
Y_AXIS then this is first strip displayed.
If SP_AXIS is Z_AXIS or A_AXIS then this
is which slice to start at. If SP_SEQ_ORDER_FL is
set then this is ignored and the first strip in the
file is the first strip plotted.
SP_PER_PAGE Size Number of StriPs PER PAGE to plot. If SP_AXIS is
X_AXIS or Y_AXIS then this is number of strips
to display. If SP_AXIS is Z_AXIS or A_AXIS
then this is ignored.
SP_RES_END Size Last strip to plot. For plotting strips on multiple
pages. The full set of strips nead NOT be
plotted. If SP_SEQ_ORDER_FL is set then this
number corresponds to the last subscript to the
Strip that is plotted.
SP_RES_OVERLAP 0 Number of StriPs to OVERLAP between succsessive pages.
This allows the same strip to be at the end of one
page and the begining of the next page. If this is
less than 0 than SP_RES_OVERLAP is set to 1/2 of
SP_PER_PAGE. The default does NOT give an overlap.
SP_OO_ASSIGNED 0 If nonzero then the Referencing for the strips in
the Original Order can be used to determine the
the Residue Number for each strip, ie use K25.
Otherwise only a strip ID will be used, ie use 25.
The referencing in the Original Order is determined
at the time that the strips were created and
requires that adjacent strips have consequtive
Res. Numbers.
SP_SEQ_ORDER_FL - If set then this file is opened and used to Re-order
the strips into the "Manipulated Order". The
Manip. Order is only used for re-ordering the
display or plot. The Original file containing
the Strips will stay in its Original Order.
2 keywords are used in the SP_SEQ_ORDER_FL 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. This keyword may
be absent and defaults to no
Unassigned.
USE_AA_CODE_3 0 Use the 3 letter name for Amino Acids if non-zero.
Otherwise the single letter code is used.
This is used for scale labels and file names.
STAPP_PAR_FL - A parameter file used with stapp program but has
several Variables which are used in ps_contour.
See also the stapp.help file.
The following Variables are used in ps_contour:
EXP_NAME, DIM_COUNT, THRESHOLD, ACQ_BASE_PHASE,
ANTIPHASE_FOLDOVER, SHIFT_TBL_TYPE, SEQUENCE,
PROG_PATH, AA_PAR_FL, EXP_PAR_FL, STAPP_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.
If STAPP_PAR_FL is used then PROG_PATH,
AA_PAR_FL and EXP_PAR_FL will be taken from
the stapp.par file.
PROG_PATH "." Path for Text files used by ps_contour, pipp, and stapp.
The ps_contour shell script which calls the
ps_contour program will set this.
The *_PAR_FL listed below allow each file to
be separately relocated by specifiing its
absolute or relative path MUST be used.
AA_PAR_FL - Filename of file containing standard definitions
of the Amino Acids. The default is hard
coded into the program. This is where
the program determines the 1 and 3 letter
codes for the Amino Acids as well as the atom
names for all of the atoms. This will NOT be
used with PROG_PATH. MUST specify full path
name or use path relative to cwd. See also
stapp.help
EXP_PAR_FL - Filename of file containing definitions about every
NMR Exp. This will NOT be used with PROG_PATH.
MUST specify full path name or use path relative
to cwd. See also stapp.help
SHIFT_FL_NM - Filename for file containing the chemical shifts.
See stapp.help and example files for the format.
Note there are two format types, the program
determines which type when reading the file.


Plot Orientation Diagrams:

Orientation: VIEW_IN_PORTRAIT 1 & SWITCH_XY_AXIS 0
This is the default orientaion, ie do nothing and get this.
Page is viewed in portrait with X and Y axis unchanged

PC----------------------+
| TM | Legend:
| +-------O | PC: Postscript Contour origin
| | |^ | PS: Postscript Scale origin
| | |^ | LM, RM, BM, TM: Plot Margins (cm)
| | |^ | 0: 2D NMR origin
|LM |X |^ RM | X, Y: 2D NMR axis
| | |^ | ^ : Scale Label Orientation
| | |^ | and default position
| | Y |^ |
| +-------+ |
| ^^^^^^^ |
| BM |
PS----------------------+




Orientation: VIEW_IN_PORTRAIT 0 & SWITCH_XY_AXIS 0
Page is viewed in lanscape with X and Y axis unchanged

P-----------------------+
| LM | Legend:
| +-------+ | P: Postscript page origin
| ->| | | LM, RM, BM, TM: Plot Margins (cm)
| ->| | | 0: 2D NMR origin
| ->| | | X, Y: 2D NMR axis
|BM ->|X | TM | -> : Scale Label Orientation
| ->| | | and default position
| ->| | |
| ->| Y | |
| +-------O |
| ->->->-> |
| RM |
+-----------------------+



Orientation: VIEW_IN_PORTRAIT 0 & SWITCH_XY_AXIS 1
Page is viewed in lanscape with X and Y axis swicthed

PS----------------------+
| LM | Legend:
| +-------+ | PC: Postscript Contour Origin
| ->| | | PS: Postscript Scale Origin
| ->| | | LM, RM, BM, TM: Plot Margins (cm)
| ->| | | 0: 2D NMR origin
|BM ->|Y | TM | X, Y: 2D NMR axis
| ->| | | -> : Scale Label Orientation
| ->| | | and default position
| ->| X | |
| +-------O |
| ->->->-> |
| RM |
PC----------------------+



Orientation: VIEW_IN_PORTRAIT 1 & SWITCH_XY_AXIS 1
Page is viewed in portrait with X and Y axis swicthed

+-----------------------+
| TM | Legend:
| +-------O | P: Postscript page origin
| | |^ | LM, RM, BM, TM: Plot Margins (cm)
| | |^ | 0: 2D NMR origin
| | |^ | X, Y: 2D NMR axis
|LM |Y |^ RM | ^ : Scale Label Orientation
| | |^ | and default position
| | |^ |
| | X |^ |
| +-------+ |
| ^^^^^^^ |
| BM |
P-----------------------+



Version 4.3.2 ( 03/15/00 )


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