| Written by Zsolt Zolnai | National Magnetic Resonance Facility at Madison |
PIXI is Copyrighted (c) 1989 by Zsolt Zolnai and National Magnetic Resonance Facility At Madison, University of Wisconsin-Madison. All rights Reserved.
You are free to use, copy, and distribute PIXI for noncommercial (this means you can't sell it) use IF:
NO FEE IS CHARGED FOR USE, COPYING, OR DISTRIBUTION.
THE PROGRAM IS NOT MODIFIED IN ANY WAY.
This program is provided AS IS without warranty, expressed or implied, including but not limited to fitness for a particular purpose.
If you find PIXI useful and wish to receive updates as they become available, then send us your name and address. We will notify you when a new version is available. We will charge you for the disk, shipping, and handling costs if you want an update.
Milo Westler
NMRFAM
420 Henry Mall
Dept. of Biochemistry
University of Wisconsin-Madison
Madison, WI 53706, USA.
Reference:
Zs. Zolnai, W. M. Westler, E. L. Ulrich, and J. L.
Markley, "Drafting Table and Lightbox Software for
Multidimensional NMR Spectral Analysis (PIXI). The
Personal Computer Workstation." J. Magn. Reson.
in press (June 1990).
IMPORTANT
In the CONFIG.SYS file the following must be present:
DEVICE=x:\path\ANSI.SYS
where x is a disk drive letter and \path\ is the path to the directory containing the ANSI.SYS file. If this is not already present, then edit the config.sys file and reboot before running PIXI.
!!NUM LOCK should be off.!!
The F1..F8 softkeys are used to toggle, on and off, spectra that are loaded
into the bit planes corresponding to the softkeys.
The ^,>,<, and v keys on the keypad (or keyboard) are used
for moving the cursor and sizing the expansion box.
The *,/ keys change the direction of movement of the expansion box
limits. The default '*' makes the box increase in size. The size
decreases after '/'.
DEFAULTS - using RETN and ESC
If PIXI gives a prompt with a default value (e. g. INTENSITIES
'i') then a RETN will accept the displayed value. To change the
value, manually type in the desired value.
ESC the normal exit to subroutines, submenus and the program. If
you do something you didn't want to do, then try pressing ESC
before killing the program.
To normally terminate the program press ESC. The program will
respond with 'Are you sure ? '. Typing a 'y' will exit the
program any other key will return to the program.
Most questions that require a 'y/n' answer will accept return for
'y' and ESC for 'n'.
!!DON'T USE THIS UNLESS YOU FEEL YOU ARE ABOUT TO PANIC!!
!!! CTRL c or CTRL break will catastrophically terminate the program !!!
CTRL ALT DEL (reboot) will terminate everything.
!!DON'T USE THIS UNLESS YOU FEEL YOU ARE ABOUT TO PANIC!!
LOADING FILES
When PIXI is executed, the initial response is a prompt for a
data file (*.DAT) to be loaded. Enter the filename [include the
.DAT extension]. See 'EDITING OF PARAMETERS AND DISPLAY'
For loading subsequent files:
ALT l load a .DAT file into a bit plane controlled by a softkey
[F1..F8]
Asks for the .DAT filename [include the .DAT extension].
Also see 'SAVING AND LOADING OF SESSIONS'
ALT u unload spectrum from bit plane. Files should be unloaded
before a new file is loaded into the same bitplane(s). The
number associated with the file to be removed can be
obtained from 'f' (see below).
EDITING OF PARAMETERS AND DISPLAY
PIXI allows for the checking and editing of the spectral parameters
associated with the .DAT file.
1. Type of spectrum.
2. Size of the original (full) spectrum in rows and columns.
3. Size and ppm limits for the actual data being loaded (this
allows for loading of subspectral files created by CHOPPER)
To check the parameters answer 'y' or 'RETN' to the prompt. A
'n' answer will continue with the loading process without changes
to the parameters.
To edit the parameters answer 'n' to the prompt at the end of the
checking process.
If 'n', then the prompting then continues:
Spectral Type - If you do not want to change the spectral type,
then answer 'n' to 'Change spectrum type ?',
otherwise answer 'y' and continue typing 'n RETN'
until the spectral type appears then answer 'y
RETN'.
For the following questions if the default value is correct then
type 'RETN' to accept it.
Enter the size of the original spectrum: - type 'RETN'
Full number of rows = ###>> Enter the number of rows in the original
full processed spectrum (before any
modification of the size by CHOPPER).
Full number of columns = ###>> Enter the number of columns in the
original full processed spectrum (before
any modification of the size by
CHOPPER).
Enter specifications of the actual data set: type 'RETN'
First Row = ###>> Enter the number for the first row or accept
the default.
Corresponding ppm = ###>> Enter the ppm corresponding to this row.
Last Row = ###>> Enter the number for the last row or accept
the default.
Corresponding ppm = ###>> Enter the ppm corresponding to this row.
First column = ###>> Enter the number for the first column or accept
the default.
Corresponding ppm = ###>> Enter the ppm corresponding to this column.
Last column = ###>> Enter the number for the last column or accept
the default.
Corresponding ppm = ###>> Enter the ppm corresponding to this column.
Are the entered values correct ? Answer 'y' if no more corrections
are desired.
CHOOSING THE DISPLAY SOFTKEY
PIXI can load up to 8 different spectra into video memory.
Spectra containing both positive and negative peaks are counted
as two spectra for the purpose of the number of loaded spectra
but both levels are manipulated simultaneously. Each spectrum
can be selected for analysis and expanded. Multiple spectra and
expansions (up to 4) can be overlaid. The prompting continues
after the checking of parameters:
4. Bit plane where positive peaks of spectrum are to be loaded
[0..8]. Use zero if no positive peaks are available or desired.
The number chosen for the bit plane corresponds to the number of
the softkey that controls the display of the spectrum.
5. Bit plane where negative peaks of spectrum are to be loaded
[0..8]. Use zero if no negative peaks are desired or available.
The number chosen for the bit plane corresponds to the number of
the softkey that will control the display of the spectrum. If
both positive and negative peaks are in the spectrum and both are
normally displayed (e. g. COSY) then, by default, either the
positive or negative softkey can be used to control the display.
NOTE: Displaying both positive and negative peaks requires two bit
planes (softkeys). For overlaying spectra, bit planes
(softkeys) [1..4] or [5..8] can be used. Spectra located in
bit planes [1..4] cannot be simultaneously displayed with
spectra located in bit planes [1..5].
HINT: If a spectrum contains both positive and negative peaks, but
the sign of the peaks is not important, then to conserve
space both positive and negative peaks can be loaded into
the same bitplane.
[F1..F4],[F5..F8]
on/off toggle switches for the display of spectra
loaded into the 8 possible bit planes e.g. F1 toggles
on and off the display of the spectrum loaded into bit
plane 1. Two sets of four different spectra can be
overlaid (each loaded into a separate bit plane). To
overlay spectra, they must all be loaded into bitplanes
corresponding to F1..F4 or F5..F8.
[SHFT F1..SHFT F8]
Select active spectrum in bitplane [1..8]. A spectrum
must be active in order to expand regions, pick peaks
or perform other functions. Only one spectrum is
active at a time. EXCEPTION: For spectra containing
both positive and negative peaks, both of the bitplanes
are active, simultaneously and are coupled.
PAGE TOGGLE
F9 selects page 1 (bitplanes 1..4)
F10 selects page 2 (bitplanes 5..8)
These keys allow rapid switching between the two sets of 4
bit planes. They do not effect the status of the active
bitplane.
NOTE: If the screen is blank, press a softkey where a spectrum is
loaded and the spectrum will appear. If not then PIXI is
waiting for a load command (ALT l, ALT o).
SAVING AND LOADING OF SESSIONS
ALT s During a PIXI session this command will save the current
loading (spectra, expansions, contour levels, etc.) in a
file (*.px). [include the .px extension]
ALT o To load a saved session (*.px). At the initial prompt type
ESC {{you will get a blank screen}}, then type 'ALT o'. The
program prompts for a *.px filename. A stored session can
be started at anytime during PIXI. 'ALT o' will delete the
current loading.
LOADED FILE INFORMATION
f file information on all files
1st window displays the loaded filenames and associated file
number for unloading (ALT u), e.g.
1 cytca
2 cytcao
3 cytcam
4
5
6
7
8
This shows 3 loaded spectra and the filenumber associated with
each.
Pressing the number corresponding to a file opens a 2nd window.
The 2nd window contains information about the softkey
[F1..F8] location of the positive (+) and negative
(-) peaks and ROI (expanded Regions Of Interest).
2 cytcao
ROESY
+ F7
- F8
Act.ROI 3
ROIs
0 1 2 3 4
5
01034
12345
At the bottom of this window is the linking of the ROI for the
'ALT n' and 'ALT p'commands.
Pressing one of the ROI numbers opens a 3rd window.
ROI 3
n1
3.004
6.005
n2
5.998
9.998
The 3rd window contains the ppm limits for that ROI.
ESC returns to the previous window.
SHIFT f file information for the active spectrum
The initial window is same as the 2nd window of the 'f'
command for the active spectrum.
ESC returns to the previous window.
CURSOR MOVEMENT - The spectrum must be active.
The cursor is moved by the arrow keys. The keys [1,3,7,9] on the
keypad are used to change the step size the cursor. The smallest
step size is 1 and the step size, and therefore apparent speed,
increases with increasing numbers.
{{ The + and - keys increase and decrease the step size and
decrease, respectively, the speed of the cursor by adjusting the
number of screen positions moved for each press of the arrow
keys.}}
SHFT k centers the cursor anytime (useful for finding cursor that
is offscreen)
EXPANSION - The spectrum must be active.
The cursor should be moved to the general area to be expanded.
l display expansion limit box
The arrow keys (no num lock) move the sides of the box.
* = The box size increases with the arrow keys (default)
/ = The box size decreases with the arrow keys
The keys [1,3,7,9] on the keypad are used to change the step
size the box limits. The smallest step size is 1 and the
step size increases with increasing numbers. The default is
for the box size to increase (*). Execute the expansion
with 'x' or 's'. ESC before 'x' or 's' is entered will
return to the current spectrum without expansion.
SHFT l Enter expansion limits by ppm values
The expansion limits can be entered manually if the ppm
values are known. Execute the expansion with 'x' or 's'.
ESC before 'x' or 's' is entered will return to the current
spectrum without expansion.
x Expand box defined by 'l' or 'SHFT l'
This results in a screen displaying the expanded region of
the spectrum with a cursor. The chemical shift limits of
the displayed region are written on the screen along with
the position of the cursor. If the cursor is not visible
then type 'SHFT k'.
s Expand box in symmetric spectra (NOESY,COSY, DOUBLE QUANTUM
etc.). This results in a split screen displaying the
symmetric regions of the spectrum with coupled cursors. The
chemical shift limits of the symmetric regions are written
on the screen along with the position of both cursors. If
the cursors are not visible then type 'SHFT k'. The active
cursor can be toggled between left and right screens by INS.
NOTE: SHFT k centers the cursor anytime
After either x or s, PIXI will prompt 'load ROI [1..9]
'. Up to 9 ROI (Regions Of Interest) expansions are
available for each loaded spectrum. Each expansion is associated
with a ROI number between 1 and 9. If it does not matter where
the next expansion is located then choose the default value for
ROI #. See the next section for details on ROI.
REGION OF INTEREST (ROI) MANAGEMENT - The spectrum must be active.
Each spectrum controlled by a softkey can be expanded into 9
Regions Of Interest (ROI). The limits for the expansions can be
done by either the 'l' box or the 'SHFT l' manual entry.
Information concerning the ROI are available from 'f' or 'SHFT
f'.
Expansion of a region requires the entering of a ROI number or
accepting the default value (RETN). This number becomes
associated with the expansion.
SHFT r display of ROI on full spectrum (ALT f). A visual
representation of the chemical shift limits of the loaded
ROI.
RULES:
Any legal ROI number [1..9] is permitted.
Unwanted ROI can be overwritten. This may change the
linkage chart (see below).
The default ROI from for the next expansion is the next
free ROI.
The default ROI from ROI 9 is ROI 9.
MOVEMENT BETWEEN ROI - The spectrum must be active.
Within the current active bitplane any ROI is accessible by
typing the number of the ROI followed by 'x' or 's'. This may be
the most versatile way of moving between the ROI. Information
about the current ROI are available from 'SHFT f' or 'f'.
The ROI are also linked such that 'ALT p' will return to the ROI
from which the current expansion was derived and 'ALT n' will
transfer to a choice of one of the ROI that were defined from the
current expansion. A linkage chart of the ROI is available from
the 'SHFT l' information window. At the bottom of the window,
the linkage chart is shown. For example, consider the following
SHFT l window:
1 cytcao
ROESY
+ F1
- F2
Act.ROI 3
ROIs
0 1 2 3 4
5
01034
12345
In this window, the number and name of the loaded spectrum is
shown along with the softkeys that control the positive (+) and
negative (-) levels of the display. The available ROIs are 0
(the full spectrum) and 1..5. The active ROI is 3.
At the bottom, the linkage chart shows that 'Alt n' will transfer
from ROI 3 to 4 making 4 the active ROI, a second 'ALT n' will
transfer from 4 to 5. 'ALT p' reverses the direction, that is
transfer from 5 to 4 and 3 to 0.
If the active region is 0, then from the linkage chart there are
two ROI that are linked by 'ALT n', 1 and 3. PIXI will prompt
for the desired ROI number.
ALT f return to full plot (ROI 0) does not reset ROI.
ALT n move to next linked ROI
ALT p move to previous linked ROI
1..9 select ROI to be displayed (MUST be followed by 'x' or
's' to update display. ESC to abort.)
INTENSITIES AND CONTOUR LEVELS - The spectrum must be active.
i intensity levels (initial default is one level at 256)
IN FULL PLOTS
Changes the intensity of the single level in the full
plot. This value becomes the lowest contour level for
subsequent expansions. A single level contour plot of
the full spectrum can be obtained by typing 'x'.
IN EXPANDED PLOTS
Asks for number of contour levels (maximum 16) followed
by values for each of the levels. Initially, expanded
regions are drawn with only one contour level for
reasons of speed. A quick idea of the desired levels
can be obtained from the full plot or by using one
contour level in the expanded region.
PEAK PICKING
The active cursor position can be stored in a file (*.PIK). This
position can be annotated by almost any character from the
IBM ASCII character set. The *.PIK files are text files
that can be edited with any word processing program. The
first column of the *.PIK file contains a number that is
determined by the symmetry relationship of the peaks within
the particular type of spectrum. The second and third
columns are the chemical shifts of the two spectral
dimensions, respectively. The fourth column contains an
ASCII character that is used to mark the peak position on
the display. The default character is the asterisk (*), but
the user is free to choose whatever character is desired
(including the extended IBM character set) to annotate the
peak. A final 256-character field is used for comments.
This simple file format allows the chemical shift data to be
ported easily to other programs such as automatic assignment
packages, databases, etc.
SHFT h Enter peak picking mode in active spectrum. Opens *.PIK
file associated with active file. Asks (somewhat
cryptically) for information regarding the ASCII character
to be used as the peak position marker.
The first question is:
Output default pick pattern?
Answering 'y' to this question will mark all of the peaks stored
in the *.PIK file as an asterick '*'. Answering 'n' will mark
the peak positions with whatever ASCII character is in the fourth
column of the *.PIK file. This can be used to annotate peaks
with information regarding assignments such as single letter
amino acid codes.
The second question is:
Input default pick pattern?
Answering 'y' to this question means that any peak to be picked
will be marked with an asterick '*' on the spectrum and in the
*.PIK file. If 'n' is answered, then every time a peak is picked
the program will prompt the user for the desired ASCII character
to be used to mark the peak. This character will be stored in
the *.PIK file. These characters are dislpayed if 'n' is
answered to the first question.
h Turn off peak picking. The screen will still show the peak
position markers until 'x' or 's' are typed or the ROI is
changed.
ENTER Write peak position marker to screen and to *.PIK file.
Typing another ENTER before moving the cursor will erase
the marker on the screen.
ALT d In symmetric spectra (NOESY, COSY, DQC, etc.) this command
toggles the coupling of the two cursors for peak picking.
If in SNGL mode, only the position at the active cursor
will be marked and written to the .pik file. If in DUAL
mode, then the symmetric positions will be marked and
written to the .pik file.
TAB Go to the next symmetric pairs of peaks. {spectrum
dependent}
SHFT TAB Undo TAB
Short command list
Key: ESC = Escape key
ALT = Alt key
SHFT = Shift key
CTRL = Control Key
RETN = Return or Enter key
F1..F8 = soft keys
+,-,*,/ = plus,minus, asterisk, and slash keys
^,>,<,v = arrow keys (keypad or arrows)
1..9 on keyboard = selection of ROI expansion
1,3,7,9 on keypad = step size of box limits and cursor movement
(1 smallest)
Arrow keys control cursor movement and expansion box limits.
ALT l Load .DAT file
ALT u Unload a file (number available from 'f')
ALT o Load old .px session
ALT s Save .px session
F1..F8 Toggle spectra in Fx on/off
SHFT F1..F8 Make spectrum in Fx active
F9 Select page 1 (bit planes 1..4)
F10 Select page 2 (bit planes 5..8)
SHFT l Enter ppm limits for expansion manually
l Box for expansion limits (arrow controlled)
x Expand selected region
s Expand selected region into split screen (symmetric spectra)
ALT f return to full plot (ROI 0) does not reset ROI.
ALT n move to next linked ROI
ALT p move to previous linked ROI
1..9 select ROI to be displayed (MUST be followed by 'x' or
's' to update display).
i Select number of contours and intensities
f File information on loaded spectra.
SHFT f Active file information
SHFT r display of ROI on full spectrum (ALT f)
SHFT h Turn on peak picking
ALT h Change peak picking marker
ENTER Enter peak position to *.pik file
(within peak picking 'SHFT h')
h Turn off peak picking
ALT d Toggle single to dual peak picking in symmetrical
spectra
Typical Session
pixi
;returns with prompt for *.DAT file
demo.dat
Change the parameters ?
n
Bitplane for positive levels [0,8]
4 ;load spectrum into bitplane 4 (controlled by F4)
Bitplane for negative levels [0,8]
0 ;no negative levels
;spectrum is displayed now
i ;want to change intensity
Level 256 >> ;current level 256
1200
;spectrum is displayed at new intensity
;now expand some region
;choose precision (speed) of cursor with numbers
on keypad (1,3,7,9)
;move cursor with arrow keys
l ;expansion box appears - use arrow keys to expand
box. type '/' to decrease the size of box or
'*' to increase (default)
x ;expands region with one contour ('s' will display
symmetric regions of symmetric regions with two
cursors)
i ;change the intensity and number of contours
number of levels 1 >>
4 ;display 4 contour levels
level 1200 >>
1200 ;enter level intensity (displayed number is
default
level 0 >>
1400
level 0 >>
1600
level 0 >>
1800
;contour plot is drawn
etc.
APPENDIX 1: CONVERSION OF *.SMX files on Bruker Aspect TO *.SAS
files for PIXI.
1). Process two-dimensional spectra in the normal manner and reduce
the file (WRED). Region files produced by CHOPPER are also legal
as PIXI files. !!RECORD the original number of rows and columns
of the transformed file (i.e., how many rows and columns are
displayed by AP2D). If the file is chopped, also record the
appropriate rows and columns of the chopped region. The upper
and lower chemical shift limits for both dimensions of the
spectrum should be recorded. You also should know what type
of spectrum you are converting (e.g. HH-COSY, HOHAHA, HSBC etc.).
2). Any post-processing such as baseplane correction (JROLLER) or
noise removal (MAKEUP) must be done before the conversion to PIXI
format.
3). By inspecting the AP2D display or a plot of the data, decide what
threshold will remove most of the noise without losing any peaks.
The number that is the lowest level (LEV) corresponds to the
threshold value. Data with intensities less than the threshold
value (or greater than for negative intensities) will be removed
from the data set. Either positive, negative or both intensity
values can be selected. If the file has been treated with
MAKEUP, select 0 as the threshold value.
4). Run THRESH and reply to the prompts. The file extensions (those
characters to the right of the '.') must be included as well as
the drive designation (e.g., =D3). The SAS extension is not
mandantory but is standard. The screen will start displaying
numbers. The numbers will begin at 0 and continue to the total
number of rows in the spectrum.
5). When THRESH is finished, transfer the *.SAS file !!AS AN ASCII
FILE!! to the AT by ZZNET.
Appendix 2. Conversion of *.SAS files to *.DAT files (SASTODAT)
The *.SAS file is an ASCII file that must be converted to a
binary (*.DAT) file for use by PIXI. Run SASTODAT on the AT
(this can be done on any AT or PS/2). Again the file extensions
should be entered. You can defer entering the parameters until
later (at the first loading of the spectrum by PIXI) or enter
them now. The Bruker 24 bit integers can be converted to PC 16
bit integers by several methods. The data can be 'cut',
'scaled', or 'logarithmically scaled'; 'cut' drops the most
significant byte (for spectra with large solvent peaks), 'scale'
drops the least significant byte (where the dynamic range of all
the peaks is small). The logarithmic choice scales 24 bit data
to 16 bit data by taking the logarithm base (~1.0004876641...) of
the 24 bit word. The intensities after logarithmic scaling are
nonlinear but the original intensities can be recovered to within
0.05% by reversing the process. The generated *.DAT file is now
ready to be used by PIXI.
The *.SAS text files can be created from any two-dimensional
spectrum by writing a program that extracts the intensities of
the peaks above some threshold value which usually is set near
the top of the noise level. Small regions of the spectrum also
can be chopped out if only a portion of the spectrum is required.
We have written a program (CHOPPER) for the Aspect 3000 computer
that extracts regions of spectra from processed two-dimensional
spectra (Zs. Zolnai, S. Macura, J. L. Markley, to be published).
The following is a generic program for generating *.SAS text
files from generic two-dimensional spectra:
Program threshold;
FOR all rows
IF row contains any element above the threshold value THEN
BEGIN
Write_to_Text_file(row_number,[EOLN]);
FOR all columns
IF intensity > threshold THEN
Write_to_Text_file(column_number,',',intensity,[EOLN]);
END;
Write_to_Text_file(0,',',0,[EOLN]);
END;
END;
Write_to_Text_file([EOF]);
END.
[EOLN] end of line sequence
[EOF] end of file character
Sample *.SAS file:
0 [EOLN]
35,3456 [EOLN]
36,5000 [EOLN]
37,4640 [EOLN]
38,3077 [EOLN]
0,0 [EOLN]
1 [EOLN]
20,5000 [EOLN]
23,545 [EOLN]
etc.
[EOF]
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