ANSIG
TUTORIAL
What is ANSIG
ANSIG is a program for viewing and assigning 2D, 3D
and 4D NMR spectra (both homonuclear and heteronuclear) of biological macromolecules,
mainly proteins. The input data for the program are frequency-domain spectrum
matrices, together with the sequence of the protein.
In ANSIG, a spectrum is viewed as 2D planes or projections
of 2D planes. Contours can be computed "on the fly", or the contours can
be loaded from precomputed contour files. The scroll bars allow interactive
and quick change of how many 2D planes one views at any one time. It is
possible to have several graphics windows open at the same time, and to
display different views and different regions of the spectra in each window.
The peak-picking and assignment of crosspeaks in
the spectra is done interactively by the user. The assignment data base
is updated automatically by the ANSIG program after each change the user
makes to the assignment data. The current assignment table and NOE list
are always available, and always reflects the current state of the assignment.
The NOE list can be output in different formats for use with other programs
for the determination of 3D structure.
Starting up the ANSIG program
Log in to your acquired SGI account. Go to toolchest
and drag the mouse down to UNIX shell. A new window should appear, this
will be your text window. At the command line type pwd ( print working
directory), this will tell you what directory you are currently in. This
should be /home/'your name'. Now you will need to create a directory which
will contain all of your angiotensin data, for example 'angio'.
At the command line type: mkdir angio
Check to see that the new directory is there by typing: ls (list)
Now go into that directory by typing: cd angio
Copy the required data either directly from the FTP
site or from your instructors file ( up to Her/His discretion) directly
into that directory: cp 'angio.data' /home/'your name'/angio
Continue to aquire all the neccessary files for your project in this
manner. Periodically check to see that the files are all allocated into
your directory by typing: ls
Now you are ready to start up the ANSIG program, type runansig and wait
a few minutes for the windows to all come up.
The ANSIG program starts up reading the following files in the given
order:
the control file, .ctl
the dictionary file, .dic
the sequence file, .seq
the spectrum description file, .spc
the crosspeaks file, .crp
If any error occurs while reading any of these files, then the program
is not properly set up. Quit from ANSIG by typing either, command quit,
and have someone help fix the problem before going on.
Giving commands
There are basically two ways to give commands. Either
you can type in a command from the ANSIG> command line in the so-called
tty window, or you can click on the commands from the graphics window using
the middle mouse button. ANSIG always starts up in tty mode. Working from
within the graphics mode has been known to be a little more user friendly,
therefore instructions will be as such. To switch from tty mode to graphics
mode, type graphics. Likewise, to change back to tty mode, click on the
command tty in the graphics menu window. You will need to be in tty mode
to exit the program with the bye command. NOTE: the bye and quit
commands are synonymous .
If all is well, type graphics from the ANSIG command
line which will send you to the graphics menu window. The mouse can now
be used to manipulate the spectra in the graphics window and to give commands
from the graphics menu window. Size the window to a convenient shape With
the middle mouse button, click on contours then dqcosy. At the ANSIG> command
line( text window) it should read that the contours are being calculated.
Now both of the ansig spectral windows should display the dqcosy spectra.
You can minimize one window now and expand the main window, or keep them
both open to look at different parts of the spectra. (Typically you want
a text window, the graphics menu window, and two spectral windows open)
A command is activated by picking the item with
the middle button of the mouse. If the command needs more arguments then
a prompt will appear in red text in the upper left of the menu box. If
you make a mistake, pick the abort command in the menu window and start
again.
Loading crosspeaks and the crosspeaks file
The crosspeaks file ( called *.crp ) is automatically created, written,
read and updated by the ANSIG program. It is in binary format and cannot
be read directly by the user. An ASCII file will have to be created manually
by the user that can later be viewed and edited. This file is intended
as a means of exporting crosspeaks files between systems with different
binary data representations. To create an export crosspeaks file:
ANSIG> CROSSPEAKS EXPORT filename
This should be performed the first time you start up the program.
Maneuvering within the spectral windows
The mouse will be utilized in moving about the spectral
windows. When the graphics input mode is on (as it should be now), it is
possible to view the different areas of the spectra by translating the
spectra within the window. Basically you can shove around the spectra in
the window using the mouse. To translate your DQ-COSY spectra, press and
hold down the left mouse button and slide the mouse. Release the button
to stop translation.
To zoom or shrink the spectra, hold down the right
mouse button and slide the mouse up or down (vertically). The spectra in
the window will scale up or down, respectively. Practice with the DQ-COSY
spectra.
The following is a subset of the online ansig manual
as developed by Per Kraulis
April 15, 1996. The full length online manual
can be utilized as well.
GRAPHICS command reference
If no arguments are given, then the GRAPHICS command activates the graphics.
Further user input is then expected from the graphics interface, while
the tty is inactive (except for output generated by ANSIG). A spectrum
window is created if there is none.
To return to the tty from the graphics, pick the item tty in
the graphics command menu, or hit the keyboard
key T.
Handling windows
A new graphics window is brought up by the command GRAPHICS
WINDOW, or by picking the item window in the commands menu.
A total of 6 spectrum display windows can be open during a session. As
long as the graphics remains opened, at least one spectrum display window
is always present together with the commands menu.
The graphics windows can be repositioned, resized (except for the command
menu window) and iconized during a session, using the usual window manager
facilities.
A graphics window is removed by selecting the item Close from
the window manager menu: Press and hold down the right mouse button while
on the window border, move to the Close item in the pop-up menu,
and release the button. The Quit command cannot be used.
GRAPHICS AREA
Sets the viewed area in the current window to encompass the current area.
This is the inverse of the command GRAPHICS CURRENT.
See also: GRAPHICS BOX.
GRAPHICS ASSIGNMENTS spectrum
Download to the graphics all assignment labels for all loaded crosspeaks
in the given spectrum.
GRAPHICS ASSIGNMENTS crosspeak
Download to the graphics the assignment label for the given crosspeak,
if it is loaded.
GRAPHICS ATTACH thisdim [ otherwindow otherdim
]
Attaches the window scaling and translation along the specified dimension
of the current window to the given window and dimension. This means that
scaling and translating the spectra in one window will also move and translate
the spectra in the other attached window.
If no arguments for the other window are given, then any current attachment
for the current window in the specified dimension is severed.
Only the F1 and F2 window dimensions can be attached to each other.
GRAPHICS BOX
Activates an interactively changeable box in the current window, whose
position when the item yes is picked defines the current area. Picking
no or abort deactivates the box without modifying the current
area.
The initial position of the box is the current area.
The box is moved by picking one side, holding down the mouse button,
and dragging to the desired position. This can be done with any side any
number of times before picking yes or no. The corners of
the box cannot be picked.
When 3D/4D spectra are present, the position of the non-plane scroll
bars control the current area set in those dimensions.
See also: GRAPHICS AREA and GRAPHICS
CURRENT.
GRAPHICS CLEAR ASSIGNMENTS spectrum
GRAPHICS CLEAR CONNECTIONS spectrum
GRAPHICS CLEAR CONTOURS spectrum
GRAPHICS CLEAR CROSSPEAKS spectrum
Clears away all graphical objects of the given kind in the given spectrum.
The crosspeak database itself is not affected. If the crosspeaks are cleared,
then all connections and assignments in that spectrum are also cleared.
GRAPHICS CLOSE
Closes the current graphics window. The last spectrum window cannot be
closed. This command can be given from the graphics by using the Close
option in the window manager pop-up menu. See also: GRAPHICS
WINDOW.
GRAPHICS COLOR ASSIGNMENTS spectrum [ red.r green.r
blue.r ]
GRAPHICS COLOR CONNECTIONS spectrum [ red.r green.r blue.r ]
GRAPHICS COLOR CONTOURS spectrum [ red.r green.r blue.r ]
GRAPHICS COLOR CROSSPEAKS spectrum [ red.r green.r blue.r ]
Changes the color of the given graphical object in the given spectrum.
The availability of colors depend on the hardware. With sufficient number
of bitplanes, the contours have different colours for positive and negative
levels, and the crosspeaks can have another color. Connections and assignments
always have the same color as the crosspeaks in a spectrum.
The color values are reals in the range [0.0, 1.0] and define the amount
of red, green and blue to use for the specified objects. If no values are
given, then the interactive color change is activated. Move the color scroll
bars to the desired position (which changes the color immediately) and
pick any object (crosspeak or menu item) to finish.
GRAPHICS CONNECTIONS spectrum
Download all connections between downloaded crosspeaks in spectrum.
GRAPHICS CONTOURS spectrum
Download contours for the given spectrum within the current spectrum area.
If the contour file(s) have been defined and are active, the contours will
be read from the file(s). If not, then contours are computed directly from
the matrix file.
If contours are computed directly from the spectrum matrix, then it
is possible to stop this by pressing the ESC key or the Q
key while the mouse pointer is inside a graphics window.
GRAPHICS CROSSPEAKS spectrum
Download to the graphics all crosspeaks in the given spectrum that are
within the current spectrum area.
GRAPHICS CROSSPEAKS crosspeak
Download the given crosspeak to the graphics.
GRAPHICS CURRENT
Sets the current area to that viewed in the current spectrum area. This
is the inverse of the command GRAPHICS AREA. The defined
current area is also output to the tty.
See also: GRAPHICS BOX.
GRAPHICS ECHO [ message... ]
Puts the given message string, if any, into the message area of the graphics
menu window. The string is processed as usual before output.
GRAPHICS MARK crosspeak
Puts the dashed-line marker on the crosspeak. The marker lines will be
present in all window dimensions which have the same expnucleus as any
of the dimensions of the crosspeak. If the crosspeak is aliased, then lines
will appear at the aliased coordinates as well.
GRAPHICS MARK logical
If given the logical yes, then the marker will appear at the place it was
at before being made invisible. If it already is visible, then there is
no change. If given the logical no, then the marker will disappear.
GRAPHICS MENU
Delete all user-defined items in the graphics menu window.
GRAPHICS MENU [ slot-number ] menu-item
Place the item in the user-definable area of the graphics menu window.
This is how one makes macros available as commands from the graphics interface.
Currently, at most 18 (2*9) items may be defined. The item is put into
the first available slot, unless a specific slot number is given.
GRAPHICS NEGATIVE logical
If the logical is yes, then all negative contours will be dark blue.
If the logical is false (default), then the contours will have the same
colour as the positive if the graphics hardware does not have enough bit
planes (8 bits). If the graphics hardware has enough bit planes (>8 bits)
then the negative contours will have the complement colour to the positive
contours.
GRAPHICS PICK spectrum
Activates the interactive graphics crosspeak picker. After this command
has been given, ANSIG asks the user to indicate a position in a graphics
window by pointing to a position and clicking the middle mouse button.
A crosspeak will be created in the given spectrum at the indicated position.
The intensity of the crosspeak will be the mean of the intensities of the
crosspeak already in that spectrum.
If the spectrum is a 3D or 4D spectrum, then the crosspeak position
in the non-plane dimensions will be set as the middle of the current non-plane
scroll bar positions in the graphics window.
GRAPHICS PLANE expnucleus1 expnucleus2
Changes the expnucleus plane of the current graphics window. The displayable
spectra will be given default views in the graphics window. See also: GRAPHICS
VIEW.
GRAPHICS REVERSE
Switches the foreground and background colors in all graphics windows.
It is not possible to select other colors than black or white for the background
and foreground.
Default: background = back, foreground = white
GRAPHICS RULER
Output to the tty the current coordinates (in ppm) of the rulers in the
current window.
GRAPHICS TOGGLE [ spectrum ]
Toggles on or off the display of all objects in the given spectrum. If
no spectrum is given, then all spectra are toggled back on.
Note that toggling does not load or unload anything in the graphics.
When a spectrum is toggled away, the graphics retains all the objects loaded
to it. The objects are just not displayed.
GRAPHICS TRACE spectrum window-dimension
The TRACE command is not properly documented, and the command contains
some bugs which have not been sorted out yet.
Display a 1D trace of the spectrum matrix for the given spectrum in
the given window dimension in the current window. The vector shown is defined
by the currently visible area in the window, and the ruler in the given
dimension. The special window is created if it does not exist.
GRAPHICS TRACE spectrum first-ppm last-ppm real-list
Display the values in a real list as a 1D trace in the given spectrum starting
and ending at the given ppm values. The points are equally spaced along
the ppm scale.
GRAPHICS TRACE
The command without parameters removes the 1D window.
GRAPHICS TTY
Switches off the graphics interface, and activates the tty. Further input
is taken from the tty rather than the graphics. This is the inverse of
the command GRAPHICS. It is the same command as picking the item tty
in the command menu.
GRAPHICS UNVIEW spectrum
Switches off the display of the given spectrum in the current window.
This command is useful to remove the display of a certain spectrum if
it is irrelevant or otherwise unwanted in a graphics window. By default
ANSIG displays all spectra it can in each window.
See also: GRAPHICS VIEW
GRAPHICS UPDATE
Forces an update of the graphics spectrum and menu windows. This can be
useful if one wants to update the graphics after having, for instance,
moved windows, without having to go to graphics mode. It may also be useful
in writing macros.
GRAPHICS VIEW spectrum fd1 fd2
Change the view of the spectrum in the current window. The given dimensions
fd1 and fd2 refer to the spectrum dimensions that are to be displayed as
the window dimension F1 and F2, respectively. The plane (expnuclei in each
window dimension) in the current window must match the chosen spectrum
dimensions.
By default, the views for the spectra in the window are chosen as sensibly
as possible. The spectrum is not viewed in the window if no plane in the
spectrum matches the graphics window plane.
See also: GRAPHICS PLANE
GRAPHICS WINDOW
The command without argument creates a window to be positioned by the user
or automatically by the windowing system.
GRAPHICS WINDOW number
The command with an integer argument changes the window which is current.
The value must be a valid window number.
GRAPHICS WINDOW xlow ylow xhigh yhigh
The command with four numerical values as arguments creates a new window
and positions it and sets the size of it according to the values given.
If the high values are higher than 1.0, then they are interpreted as pixels,
otherwise as fractions of the total screen size. The x (horizontal) and
y (vertical) coordinates of the lower left corner of the window are given
first, followed by the coordinates of the upper right corner.
Per
Kraulis 16 Apr 1996.
Graphics command menu
The items in the graphics command menu that can be picked only when the
graphics interface has been activated (command GRAPHICS).
This is a listing of the most useful commands for a small peptide.
tty
Activates the tty input mode. This is the inverse of the command graphics.
This can also be used when ANSIG asks the user for some input while
the graphics is activated: control will temporarily be turned over the
tty, and the user can type the answer using the keyboard. This is the way
to assign a non-sequence name to a crosspeak, for example.
yes
Used to answer various questions when the graphics is activated.
no
Used to answer various questions when the graphics is activated.
current
Defines the visible area (including scroll bars, if any) in the current
window as the current spectrum area. Useful before making contours or downloading
crosspeaks. This is the inverse of the area item.
Note that the scroll bar positions (if any) is relevant when setting
the current spectrum area.
area
Forces the visible area (including scroll bars, if any) in the current
window to be that of the current spectrum area. This is the inverse of
the current item.
box
Activates a box in the current window for the user to interactively position.
When the yes item is picked, the area encompassed by
the box (and the scroll bars, if any) is defined as the current spectrum
area. If the abort item is picked, then current spectrum
area is unchanged. The initial position of the box is the current spectrum
area.
ruler
Outputs the current position of the rulers in the current window to the
tty.
window
Creates a new spectrum window, to be positioned and size interactively
by the user.
abort
Aborts any active input, command, macro or AL procedure. Control is returned
to the user.
The abort command only stops the execution of the command if it is waiting
for input. It cannot stop the execution of the command if it is running.
contours spectrum
Downloads contours for the given spectrum in the current spectrum area.
If contour file(s) have been defined and are active, then contours will
be read from the file(s). If not, then contours are computed directly from
the spectrum matrix. If contours are computed directly from the spectrum
matrix, then it is possible to stop the execution by pressing the ESC key
or the Q key while the mouse pointer is inside a graphics window.
crosspeaks spectrum
Downloads the crosspeaks for the given spectrum within the current spectrum
area.
connections spectrum
Downloads all connections between the already loaded crosspeaks in the
given spectrum.
assignments spectrum
Downloads all assignment labels for the already loaded crosspeaks in the
given spectrum.
color contours spectrum
Change color interactively for the contours in a given spectrum.
color crosspeaks spectrum
Change color interactively for the crosspeaks (and their connections and
assignments) in a given spectrum.
Three color scroll bars appear in the commands menu window which determine
the color for the given graphical objects. The scroll bar positions can
be changed while they are visible. To exit, pick any object, except the
abort item, which will change the color back to its
original value.
clear contours spectrum
clear crosspeaks spectrum
clear connections spectrum
clear assignments spectrum
Clear away all graphical objects of the given kind from the given spectrum.
If the crosspeaks are cleared, then the connections and assignments in
that spectrum will also be cleared.
This command does not affect the crosspeak data itself in any way, just
what is currently visible on the graphics display.
plane expnucleus1 expnucleus2
Changes the expnucleus plane of the current window. The views of the spectra
will be set to their default values within this window.
trace spectrum dimension
The TRACE command is not properly documented, and the command contains
some bugs which have not been sorted out yet.
A special window for 1D traces is brought up. In it is displayed the
1D trace of the given spectrum along the position of the ruler in the given
window dimension in the current window. The length of the trace is the
same as the length of the chosen ruler seen in the current window.
view spectrum dimension1 dimension2
Changes the plane of a spectrum that is to be viewed in the current window.
toggle spectrum
Toggles on or off the display of the graphical objects in a given spectrum
in all windows.
This is a quick and completely reversible way to reduce the clutter
on the display. The objects are not cleared, and may be redisplayed again
by toggling the spectrum again. The command GRAPHICS TOGGLE switches
on all spectra again.
The keyboard digits can be used instead: Hit the key followed
by a digit key. Key '1' toggles the first spectrum, '2' the second, and
so on. Key '0' toggles on all spectra.
1H 15N 13C 13CO 31P
To be used as arguments for the plane. The list contains
all expnuclei implemented in the ANSIG program, regardless of which expnuclei
are actually present in the spectra.
delete crosspeak
Deletes a crosspeak from the database and from the graphics. The crosspeak
must not have any connections or assignments.
merge crosspeak1 crosspeak2
Merges two crosspeaks into one. At most one of the crosspeaks may have
connections or assignments.
connect crosspeak1 crosspeak2
Connects two crosspeaks along a dimension.
symmetry crosspeak1 crosspeak2
Sets the two crosspeaks to be symmetry-related.
correspond crosspeak1 crosspeak2
Sets the two crosspeaks to be corresponding.
disconnect dimension crosspeak
Removes the given crosspeak from its connections in the given dimension.
remove connect crosspeak
remove symmetry crosspeak
remove correspond crosspeak
remove assignments crosspeak
Removes the given data for a crosspeak. The connections and assignments
in all dimensions are removed Warning: The removal of assignments
are propagated along the connections as usual, so it is usually a good
idea to remove all connections first.
pick spectrum
Creates a crosspeak in the given spectrum at the indicated position. The
command asks the user to indicate the position in the spectrum, and this
is done by pointing to the position in any graphics window and clicking
the middle mouse button. The spectrum must be viewed in the graphics window.
It is possible to translate and scale the spectrum and change the non-plane
scroll-bars (if any) before pointing to the position.
For 3D and 4D spectra, the position in the non-plane dimensions will
be taken as the middle of the currently displayed volume, i.e. the middle
of the non-plane scroll bars.
The crosspeak is not integrated automatically. The intensity value given
to it corresponds to the average of the already existing crosspeaks in
that spectrum.
auto crosspeak
Invokes the auto AL procedure defined for the spectrum the crosspeak is
in. The AL procedure must have been compiled
and set for the spectrum using the SET AUTO command.
move crosspeak
Switch on interactive move of the given crosspeak. The crosspeak must not
have any connections or assignments.
A white moveable crosspeak appears when this command is activated. The
moveable crosspeak object is moved by clicking the middle mouse button
while pointing to it, and dragging it to the new position, and then releasing
the mouse button.
The data for the crosspeak in the database is not updated until the
user picks the yes item in the command menu. If the
abort or no items are picked, then
the crosspeak data is not updated.
mark crosspeak
Put marker lines at the coordinates of the crosspeak. The lines are dashed,
and cannot be picked. The lines appear in all windows at all coordinates
specified by the crosspeak. If the crosspeak is in a spectrum with aliased/folded
dimensions, then the lines also appear at the aliased/folded positions.
mark yes
mark no
The marker can be switched on and off by picking the yes
or no items instead of a crosspeak.
clean crosspeak
Removes all connections and assignments for a crosspeak in such an order
that the assignments of no other crosspeaks are affected.
spectrum list
The spectrum names are filled in automatically as the first 8 spectra in
the spectrum description file. No other spectra are available on the graphics
display.
To change this, one needs to exit from ANSIG, and edit the spectrum
description file so that the desired 8 spectra appear first in it.
If a spectrum name is picked on its own, then the command SHOW
SPECTRUM is executed, i.e. all information about the spectrum is output
to the tty.
deassign sequence dimension crosspeak
deassign residue dimension crosspeak
deassign nucleus dimension crosspeak
Remove the assignment in the given field and dimension for a crosspeak.
The change is propagated in the usual way.
sequence string dimension crosspeak
Put the given string into the sequence field in the given dimension for
a crosspeak. The string can be given by picking a sequence name in the
sequence scrolling list, or by picking the tty item
and typing in the string using the keyboard. The usual consistency checks
for the combined assignment is done, and the change is propagated as usual.
residue string dimension crosspeak
Put the given string into the residue field in the given dimension for
a crosspeak. The string can be given by picking a residue name in the sequence
scrolling list, or by picking the tty item and typing
in the string using the keyboard. The usual consistency checks for the
combined assignment is done, and the change is propagated as usual.
nucleus string dimension crosspeak
Put the given string into the nucleus field in the given dimension for
a crosspeak. The string can be given by picking a nucleus name in the nucleus
scrolling list, or by picking the tty item and typing
in the string using the keyboard. The usual consistency checks for the
combined assignment is done, and the change is propagated as usual.
F1 F2 F3 F4
The F dimension items are to be used as arguments for several commands
in the graphics command menu. For a 2-D experiment only the F1 and F2 planes
will be utilized.
sequence list
The names of the sequence residues and their types are given in a scrolling
list. Use the scroll bar to move the list.
These items are to be used as arguments for the assignment command menu
items.
If a sequence or residue item is picked on its own, then the command
SHOW SEQUENCE or SHOW RESIDUE is executed with the relevant
item as argument, i.e. all information about the sequence residue or residue
type is output to the tty.
nucleus list
The names of all nuclei in all residues in the dictionary are collected
in lexical order in the nucleus scrolling list. It it controlled by the
same scroll bar as the sequence list, although it is really logically
independent of it.
user menu
The user menu can be filled with macro names or other strings (max 12 characters)
by the user.
This is how macros are made easily accessible from the graphics. If
the item is picked, then that string is executed as if it had been entered
as a command. This means that the macro is activated simply by picking
the menu item. See also: GRAPHICS MENU
Quick commands from GRAPHICS menu
When the graphics has been activated, then some commands can be issued
by one keystroke as well as by picking the item in the command menu.
Zoom in on one of the NHCH crosspeaks in the DQ-COSY
spectra.. Choose pick and click on dqcosy, position the arrow as
close to the middle of the crosspeak and then click (middle button). An
X should appear now where ANSIG thinks there is a crosspeak. If you flubbed
this up or would like to move it elsewhere, pick move and click
on the crosspeak (it will turn white) then ‘move’ it with the mouse to
the spot you really wanted. Once it is in place then hit yes.