If you run WHAT IF, you see a large series of options
in the text window. The options above the line are called general options,
and the options below the line are specific for the currently active menu.
(At the beginning there is nothing below the line, you first have to type
the name of the menu you want to use.) The group of options above the line
are called the `general menu'.
The general menu holds three classes of options:
1) Options to pass control to another menu;
2) Control options like FULLSTOP, percent, exclamation mark, etc.;
3) Options that are always useful and/or often used.
Some of these options are in the main menu, which you see in the
text window when you just hit RETURN. Several others are in
the menu called GENMEN. These are the less frequently used options, which
are nonetheless potentially useful no matter in which menu you are presently
working.
Despite being in another menu, you don't have to go
to that menu to run the options in it. They are always active. You
have to go to GENMEN, however, if you want to get help or one-line help (SHORT)
for general options, and automatic input command correction will only
work when you are actually in the GENMEN menu.
The WHAT IF main menu looks roughly like:
HELP INFO SHELL GENMEN END $.. %.. !.. SCRIPT
DOLOG NOLOG GO FULLSTOP LISTA LISTR HISTOR GETMOL
GRAFIC GRATWO GRAEXT COLOUR PLOTIT USEGRA ITMADM LABEL
SOUP 3SSP ACCESS ANACON BUILD CHECK CHIANG CLUFAM
DGLOOP DIGIT DOSELF DRUG DSSP ELECTR EXTRA HBONDS
HSSP MAP MODIFY NEURAL NMR NOTES OTHER PROTON
QUALTY REFINE SCAN3D SCNSTS SEARCH SELECT SEQ3D SETPAR
SETVDW SHOENT SPCIAL SUPPOS SYMTRY TABLES WALIGN
WATER XRAY
ANATRA TRAMOV GROMAC GRID
The top two lines hold the help and option-control related options:
E: HELP Gives help about options
INFO Gives extensive help about options
SHELL Opens a system shell
GENMEN Looks at all the other general options
END Goes back to the previous menu
$ Execute a shell command directly
% Executes commands from a different menu
! Repeat a previous command
SCRIPT Executes commands from a script file
DOLOG Opens the log file
NOLOG Closes the log file
GO Passes control from the text window to the graphics window
FULLST Ends WHAT If execution the neat way
LISTA Lists all information about 1 residue
LISTR Lists the sequence of all protein, nucleic acids, and sugars
HISTOR Shows recently executed options.
GETMOL Reads in a PDB file
The third line holds the graphics-related options:
GRAFIC General menu for the graphics options
GRATWO Two-dimensional graphics menu
GRAEXT Fancy graphics menu
COLOUR Menu to colour atoms and residues
PLOTIT Plotting menu (mainly postscript and GIF files output)
USEGRA Menu for user-defined MOL-object generation
ITMADM Menu for the administration of MOL-objects/items
LABEL Atomic-labelling menu.
The following commands all bring you to another menu. Soup is the most important
menu. Some other menus are given almost alphabetically:
SOUP Soup manipulation menu
3SSP Multiple protein structure superposition menu
ACCESS Menu for accessibility calculations
ANACON Contact analysis menu
BUILD Ab initio protein building menu
CHECK Structure validation menu
CHIANG Torsion-angle menu
CLUFAM Clusters and families menu
DGLOOP 3D-fragment database menu
DIGIT Menu for reconstructing molecules from stereo pictures
DOSELF This menu is only meant for WHAT IF maintenance
DRUG Drug-design, docking, etc
DSSP Menu to work with DSSP (or its emulator)
ELECTR Menu to work with DelPhi (electrostatics)
EXTRA Menu that does some other funny things
HBONDS Hydrogen bonds menu
HSSP Menu to work with HSSP files
MAP Handling menu for electron density and other map types
MODIFY Mutation and debump menu
NEURAL Neural network toy menu
NMR Menu with NMR specific options
NOTES Menu to make notes with amino acids
OTHER Yet another menu that does funny things
PROTON Menu to do proton-specific things
PKA pKa calculation menu
QUALTY Packing quality control menu
REFINE Structure refinement/regularization menu
SCAN3D Relational protein database module
SCNSTS Statistics on SCAN3D and DGLOOP groups
SEARCH Menu to search in the soup
SELECT Nearly obsolete menu to select proteins for SCAN3D
SEQ3D Menu to regenerate the internal database
SETPAR Menu to change parameters
SETVDW Van der Waals radius menu
SHOENT Menu to look at the internal database
SPCIAL Menu that you should not use without reading the source code
SUPPOS Protein structure superposition menu
SYMTRY Menu to work with crystallographic symmetry
TABLES The spreadsheet menu
WALIGN Menu to work with sequences (has menu sub-menus)
WATER Menu to work with water molecules
XRAY Menu with X-ray specific options
DGEOM Distance geometry toy menu
The last line lists some interfaces to external programs:
GROMAC Menu to work with the GROMACS EM/MD program
ANATRA Trajectory analysis menu
TRAMOV MD trajectory movie menu
GRID Menu to work with Goodford's GRID program
The options to read coordinates should actually be in the SOUP menu,
which is where they are described. However, these options are
so important that we decided to make several of them general options, so you
can run them, regardless of which menu you are in.
See also the SOUP chapter.
The most important command in WHAT IF is GETMOL. It is used to read
PDB files. After GETMOL, you will be prompted for the file name. You can
type the name of any PDB file. Include the path in the name, unless the file
is in the present directory, or in your standard PDB directory. If
this latter possibility does not work, ask your WHAT IF manager to
check the file CCONFI.FIG in the dbdata directory. You do not need to type
the .pdb or .brk extension to the file name.
After the file is found, you are prompted for the set name. Here, everything is
allowed. If you just type return, the set name will be the same as the file
name, which is probably what you want.
If you ask for a PDB file by giving its PDB-assigned four-letter code, but
it does not exist, WHAT IF will try to get it from my (Gert Vriend's)
computer, dump it in your local directory, and read it. This facility
often doesn't work because of firewalls, non-installed perl modules, etc.
GETMOL actually belongs in the SOUP menu, but it is so important that we
made it a generally accessible option.
The command GETMLS will prompt you for a file name. All PDB files listed in that
file will be read using the GETMOL command. See the NMR chapter for
more details. This option requires complete and correct file names. It cannot,
like GETMOL, correct your file name or get your file from the PDB, or ...
The START command will load a small protein molecule (crambin) without
needing to know
where the PDB files are stored. START obtains this molecule from the
WHAT IF internal database.
WHAT IF always allows you to inspect the presently available sequence
information and coordinates, both for the molecule(s) you are working
on and for all of the other molecules in the database.
We distinguish three sets of options:
1) looking in the database;
2) looking at sequences;
3) inspecting the molecule(s) you are presently working on.
Most of these options are explained in greater detail in the SOUP menu.
The LISTR command makes WHAT IF show you the entire sequence of the soup.
See the chapter on the SOUP for more information.
The LISTRR command will
prompt you for a residue range, and show for that range the internal
residue number, the residue type, and the original name/number as read from
the PDB file. See the chapter on the SOUP for more information.
The LISTA command can be used to look at atoms, in residue groups. WHAT IF
will prompt you for a residue range, and will then show for every requested
residue both the amino acid information such as name, type, etc. and the atomic
information such as coordinates, B-factor, Van der Waals radius, colour (if
already set), charges (if already calculated) etc. This option also works
on drugs, water, etc.
See the chapter on the SOUP for more information.
The LISTAA command functions similarly to LISTA, the difference being that
LISTA prompts you for only one range of residues, whereas LISTAA will prompt
you for multiple ranges. See the chapter on the SOUP for more information.
Sometimes one wants to find a sequence pattern, e.g.
Arg-Gly-Asp in a large structure. The SHOPAT option can help with
this. SHOPAT prompts you for three residue types (you can give
multiple types at each position). For every occurrence of the pattern
the first position will be listed.
The sidechains of all matching patterns will be displayed.
You have to give patterns of length 3. If you want patterns of length
2, use ALL as residue type at position 3 in the pattern. In this case,
however, an accidental occurrence of your dipeptide pattern at the
C-terminus will go undetected.
Normally, the command LISTR lists the sequence, for example, like:
The sequence of proteins, sugars and nucleic acids:
Molecule number 1
1- 10 THR THR CYS CYS PRO SER ILE VAL ALA ARG
11- 20 SER ASN PHE ASN VAL CYS ARG LEU PRO GLY
21- 30 THR PRO GLU ALA ILE CYS ALA THR TYR THR
31- 40 GLY CYS ILE ILE ILE PRO GLY ALA THR CYS
41- 46 PRO GLY ASP TYR ALA ASN
The magical command:
SETWIF 1 0
will tell WHAT IF to use 1-ltter code rather than 3-letter code. The same
example output will then look like:
The sequence of proteins, sugars and nucleic acids:
Molecule number 1
1- 46 TTCCPSIVAR SNFNVCRLPG TPEAICATYT GCIIIPGATC PGDYAN
You put WHAT IF back to 3-ltter code with similar magic:
SETWIF 1 1
Three-letter code is the default. This magic influences many, but not
all WHAT IF options that list residue types. Clicking a C-alpha in the
graphics window, for example, will always show the amino acid type in
3-letter code.
The APROPO command will execute the corresponding command
in the WHAT IF configuration file CCONFI.FIG. At this moment my
CCONFI.FIG file holds:
firefox http://swift.cmbi.kun.nl/writeup/
So, APROPOS will open a browser window with the WHAT IF writeup page
in it.
The AUTOON command will make WHAT IF create a (new) file SCRIPT.FIL. Subsequent
commands to WHAT IF are echoed to this file. After some minimal
editing, it can be used as a script file for the SCRIPT option. (See also the
AUTOOF and SCRIPT options.)
The AUTOON command will make WHAT IF log your commands to the file SCRIPT.FIL.
The AUTOOF command will close this file. You will have to edit
this file a little, since it is not yet automatically valid as a
script file. (See the SCRIPT option.)
The DOLOG command makes WHAT IF prompt you for the name of a log-file,
and for a comment to be written in this file. Thereafter, all relevant
information written to the terminal/text-window will also be
echoed to this file. (See also NOLOG and the chapter on logging
in this writeup.)
The DOLOG command makes WHAT IF prompt you for the name of a log-file.
The NOLOG command will close this file. Thereafter, you can
(for example) print the file with any valid print command preceded by a
dollar. (See also the chapter on logging in this writeup.)
The HISTOR command logs commands you recently
executed. For a thorough explanation see the chapter on logging
results.
The SHELL command will generate a new window for you.
You return from a subprocess to WHAT IF by typing exit.
You then get back into WHAT IF exactly where you left it, and
nothing will have changed.
I think this command is no longer useful.
The INFO command can be used to read the part of the writeup that deals with
a certain command. Just type:
INFO XXX
in which XXX stands for any option in the present menu. You will get at the terminal
the introductory paragraph from the chapter containing XXX, and
the paragraph that deals with the command XXX itself.
INFO should not be used for general options. But if you do it anyway,
you will get the introductory paragraph of the chapter for the current menu,
followed by the help for the option requested.
The HELP command can be used to get a limited amount of
help for a given command.
Just type:
HELP XXX
in which XXX stands for any option in the present menu, and you will get
some help for the command XXX.
The SHORT command will make WHAT IF show you a list of all the commands
available in the current menu, followed by a short description
of what that option can do for you. SHORT is now
implemented in almost all menus.
The MAN-K command (UNIX users can also type man -k) can be used to search
for all SHORT help lines containing a given keyword. Just type:
MAN-K XXX
in which XXX stands for any text string, and you will get
a list of all lines in all SHORT listings with XXX in it,
complete with the names of the matching menus.
The FIND command can be used to get help for an option that is not in the
current menu. Just type:
FIND XXX
in which XXX stands for any option, and you will get
some help for the command XXX.
The command SHORTT (with two Ts) gives short help about general options.
The NOVICE option toggles the mode in which you automatically get
HELP presented for every non-general option that you use.
As the name suggests, this option is meant for new users.
This option only works inside a menu. You
would get help text if you use SETACC inside the ACCESS menu, for example, but
the option %SETACC will not automatically provide the SETACC help
text, nor will general options such as GETMOL, LISTA, etc.
If you want to execute a UNIX command, you can first give the
SHELL command
in WHAT IF, and then do what you want to do in the new window. If
you only want to execute a single command, it might be easier to just
type this command preceded by a dollar sign. WHAT IF will strip the leading
dollar sign from the command line, and pass the rest on to
the operating system. If you
are executing such a process, you can terminate it with control-C (or
whatever control sequence you normally use to break a process). This
will terminate the execution of the command, and bring you back to
WHAT IF.
If you know that a command exists, but forget in which menu it is, or do
not want to go to that menu, you can execute it anyway by prefixing
it with a percent sign. E.g. typing %SHOSOU in the GRAFIC menu will
list the present contents of the soup.
The AUTO% command will automatically try a % sign in front
of every option that it cannot execute otherwise.
Use AUTO% again to toggle back to the normal mode of operation.
When using the AUTO% option, you cannot use type-ahead after a
command that can only be executed after the automatic addition of
a prefixed % sign.
The default for this option is ON, i.e., WHAT IF starts with AUTO%
used once already.
The command DUTCH will make WHAT IF talk Dutch.
Not all messages have been translated, so WHAT IF will sometimes
use one or two English sentences, but most will be Dutch.
WHAT IF's Dutch is sometimes a bit funny. That is because a large
fraction of the program messages were translated by WHAT IF itself.
The command ENGLISH will force WHAT IF to talk English. This
option is only useful if you changed the default language
earlier in the session. English is the default language.
One day, the FRENCH command will make WHAT IF talk French.
At the moment, only the prompt becomes French.
One day, the SPANIS command will make WHAT IF talk Spanish.
At the moment, only the prompt becomes Spanish.
The HISTOR command will show you the command history.
But note that many options still don't get logged in the history file.
In many places in WHAT IF parameters like line thickness, number of dots
per sphere, radius of water, cutoff radius for distance calculations, etc.
may seem somewhat arbitrary. I spent a lot of time thinking about good default
values, but if you disagree with my choices, you can go into
the parameter-setting menu with the SETPAR command. The parameter menu
has many parameter submenus in it.
Many menus include a PARAMS command, which takes you into a special menu
to modify the parameters specific to the current menu. A few parameters
function globally in WHAT IF, and are therefore hard to place in any
particular PARAMS menu. These parameters are stored in the general
parameter menu, which you access with the SETPAR command.
The following commands are found in that menu:
Colour of lines made with screen option .LINE
Line type for the lines made with screen option .LINE
Amino acid output in 1- or 3-letter code flag (about half of the options
in WHAT IF listen to this flag, the others just do what they like.).
Amount of sequence output flag in SCNSDB menu (a rather useless
parameter).
Bump/contact distance between Van der Waals radii
Default B-factor. This is used if there is no B-factor
in the coordinate file, and when `dreaming up' new atoms.
Do/don't use interchain disulphide bridges.
Do/don't use covalent neighbours in BUMP/CONTAC-like options.
In many places in WHAT IF parameters like line-thickness, number of dots
per sphere, radius of water, cutoff radius for distance calculations, etc.
may seem arbitrary. I spent a lot of time thinking about good default
values. But if you disagree with my choices, from many
menus you can go directly to the corresponding
parameter setting menu with the PARAMS command.
See SETPAR to get an overview of most of the available parameter menus.
Most of WHAT IF's internal parameters are stored in one big array.
These parameters are numbered. The file PARAMS.FIG (in the
dbdata directory)
holds their initial values. You can poke new
parameter values directly into these parameters with the SETWIF
command. I strongly recommended that you do not use this option
unless you are desperate: SETWIF does not check your values, and
setting incorrect values can lead to a program crash.
The SHOWIF command will prompt you for the number of a parameter
(see SETWIF). It will then show the documentation for it.
The obtusely named IUKKEL command will make WHAT IF activate the
SAVSOU option automatically (see the SOUP chapter) after every 50-th
option that you execute. I happens after every 10-th option if you work in debug
mode. Debug mode is default at the CMBI, but not anywhere else.
WHAT IF allows you to rename commands. Start with the > sign,
followed by a real command name. Continue on the same line with a > sign
followed by the new name for this command. This renames one command.
To use the new command name, type
the < sign first, then the new command name.
Example:
>LISTA>TYPE ATOMS to rename the LISTA command TYPE ATOMS
<TYPE ATOMS to use the new TYPE ATOMS command
The new command can be used only in the original command's menu.
You can rename up to 100 commands. Renamed commands are
not be remembered from the one WHAT IF session to the next, but
you can make a SCRIPT file to remember them.
Blank characters are part of the command. So, if you rename a command
with
> LISTA > TYPE
then only '< TYPE 13' and not '<TYPE 13' will execute the LISTA command. In
other words, the blank between > and TYPE is also needed between < and TYPE.
You can use the commands >> or << to get a listing of all renamed commands.
The commands <, >, ., !, dollar, and % cannot be renamed.
If you like to rename commands, I strongly suggest that you write a script file
to do the renaming.
If you type an exclamation mark (!) followed by one or more characters,
the last issued command starting with these characters will be repeated.
You can use the hidden command .P (period, P) to get a list of the last
100 commands. Instead of an exclamation mark you can also use a period (.).
If you type a period (.) followed by one or more characters,
the last issued command starting with these characters will be repeated.
You can use the hidden command .P (period, P) to get a list of the last
100 commands. Instead of a period you can also use an exclamation mark (!).
For the command >, see under the command <.
The SCRIPT option can be used to play a script of pretyped commands.
This option is extensively described in a separate chapter entitled
SCRIPT FILES. You are urged to read this chapter first, because SCRIPT
files are a bit tricky.
The LSCRIP option can be used to run a script of pretyped commands over
a set of PDB files.
This option is extensively described in a separate chapter entitled
SCRIPT FILES. You are urged to read this chapter first, because LSCRIP
is a bit tricky.
If you use the MAKMOL command in a LSCRIP script, WHAT IF will each time
MAKMOL is executed write the next number (1,2,3,... etc, for ever) tag to
the end of the file name.
The TEACH command is obligatory as the first command in any teaching script.
(See the chapter on teaching scripts; and the workshop website for more information.)
Whenever you use a menu command you go one menu down in the menu tree.
You can go back to the menu you came from with the END command.
There are several obvious synonyms for this command.
Whenever you use a menu command you go one menu down in the menu tree.
You can go all the way back to the first menu with the QUIT command.
The FULLSTOP command (only FULLST needs to be typed) is the preferred way
to terminate a WHAT IF session. It will stop WHAT IF and bring the graphics
device back to its normal state, which is good for the next user.
Especially on Evans and Sutherland equipment, it is important to use this
option instead of control-Y or control-Z, or any other harsh command.
WHAT IF has an in-built empty menu. You can use this to write your
own options, without having to worry about menu administration,
or the creation of pull-down menus. The MYMENU command fetches this menu for you.
See the EXTRA menu.
In the default situation, i.e., that is how WHAT IF is delivered to you,
this MYMENU is disabled. See the chapters at the end of the writeup for
notes on the activation of this menu.
The MORE command shows up in about 10 menus. If MORE is typed the
number of available commands in that menu will increase. MORE can be
reversed with LESS. The main aim of the MORE and LESS commands is to let the
user concentrate on the most important options.
The LESS command reverses the action of MORE.
(See the MORE command above).
There are two ways to communicate with WHAT IF. You can type commands
in a text window, or you can work interactively in the graphics window.
With GO, you pass control from the text window to the graphics window.
In the graphics window you pick CHAT to get back to the text window.
The EDT command will prompt you for a file name, and it will get this file
in the editor. Which editor is chosen is determined by the editor record
in the CCONFI.FIG file. You said what your favourite editor was when you installed
WHAT IF. Remember?
Sometimes one would like to start a completely new session (simply
because that would be faster than cleaning up the soup, the graphics,
etc). INIALL does just that. Running INIALL is equivalent to getting
out of WHAT IF with control-C or FULLST and starting again.
When you are working in a menu, WHAT IF can correct mistyped options
in that menu. To do so, it tries several heuristics:
1) The commonest three-letter code in this menu (e.g. TAB for the
TABLES menu, GRA for the GRAFIC menu, etc.) will be added to the
head or the tail of this option.
2) The first three characters and the last three characters of the
name are swapped. Five-character commands are padded, and both possible
swap combinations are tried.
3) All letters O are replaced by numerals 0 or vice versa.
4) All letters I are replaced by numerals 1 or vice versa.
5) All single character deletions, insertions and typographical errors are tried,
and each time the results are compared with all options in this
menu. If a single match is found, it is used. Sometimes
double insertions, deletions or typos can be corrected too.
6) All pairs of characters in the input option are swapped. If there
is exactly one swap that leads to exactly one valid option, it is used.
However, the above option correction only works for options that
are found in the menu in which
you are working. General options are not corrected.
This option does the same as SPCIAL.
This option does the same as GRPINI in the DGLOOP menu which in turn
does the same as INIGRP in the SCAN3D menu.
This option does the same as QUALTY.
Horrible misspelling of GRAFIC and GRAPHIC.
The following commands all are always active. They aren't grouped as
every grouping would be artificial. Just sit down one day, and mark the
options you think you like.
The ANGLE3 command will prompt you three times for an atom.
First, you will be prompted for the atom in the middle, i.e. the atom
at which the angle is calculated. Thereafter you will be prompted
for the atoms 1 and 2.
ANGLE3 will calculate the angle going from atom 1 to
the middle atom and then to atom 2.
For each atom WHAT IF will prompt you first for the residue number and then
for the atom in that residue.
The command DIST will prompt you for two atoma. It will calculate
the distance between those two atoms.
For each atom WHAT IF will prompt you first for the residue number and then
for the atom in that residue.
Normally, WHAT IF does its graphics via MOL-objects and MOL-items. After the DIRECT
command, however, molecules, residues and atoms are always updated
immediately if modified. Other graphics, such as, for example, H-bonds, are still put into
MOL-items. This option is in the GRAFIC menu, but can be activated from
every menu.
See the GRAFIC menu.
When you inspect interatomic distances interactively, WHAT IF will draw a line
between the two atoms, and display the interatomic distance at the midpoint
of this line. This line, and the distance, will be updated continuously. The
DSTOFF option will selectively remove all lines and distances from the
screen, and will stop them from being continuously updated. Clicking
'No Label' in the
graphics window once will do the same, but will also remove several other
interactive graphics items from the screen (i.e. NAYB, simple interatomic
lines, etc).
The MINMAX command makes WHAT IF prompt you for a residue range, and
then determine the extreme values of the coordinates in this
range. It will also determine the centre of gravity of this range. You will
then be asked if you want to recentre the SOUP. If you answer YES, the
whole SOUP will be shifted so that the centre of gravity of
the given range will be at the coordinate origin, (0, 0, 0).
Be aware that symmetry operations will no longer function properly
after you execute this option.
The SHOCEL command will make WHAT IF list all kinds of cell-dimension
information. The cell as read from the PDB file is listed together
with the cell reconstructed from the PDB SCALE records.
Additionally, WHAT IF uses artificial cell dimensions from GRID maps, DelPhi
maps, surface maps, etc. SHOCEL will also summarize the artificial cell
dimensions that come with those maps.
The main menu has several so-called hidden commands.
The CENXYZ command makes WHAT IF prompt you for the coordinates
of a point in space. This point will become the new centre of the graphics
screen.
The CHESS command will start a 1100 ELO rating chess program. (At least, if
you activated it when you installed WHAT IF.) This command should only be
used when your boss is on holiday.
The CHOOSE command will prompt you for ranges. Every subsequent command
that would normally prompt you for multiple ranges will now no longer
do so, but will use those you gave the CHOOSE command.
Use CHOOSE again to select new ranges.
Use NEWRNG to deactivate the ranges set with CHOOSE. After NEWRNG
WHAT IF will prompt you again every time ranges are needed.
Options that only require one residue or a single range of residues
as input are not affected by the CHOOSE and NEWRNG commands.
The NEWRNG command will deactivate the automatic ranges set with
the CHOOSE command.
The command FOOOOD will make WHAT IF tell you time and date.
This information can be combined with the rumblings from your belly to
see if it is time to eat, and whether the canteen is open today.
The more serious equivalent of FOOOOD is TIME. This option can even be used
from the graphics window.
Several WHAT IF options will open files for editing. Which editor
is used is determined by your choice when you installed WHAT IF.
The default editor is stored in the file CCONFI.FIG.
The SETEDT command allows you to use another editor
for the duration of this WHAT IF run. Please make sure that you
use only editors that stop WHAT IF execution while they are
active (or give the editor some flags to force this behaviour).
If you don't do this, there is no sense in editing input parameters, because
WHAT IF would already be running with superseded parameters while
you are still pointlessly changing them.
On X11 systems only you can (at the cost of rotational speed) increase the level
of elaboration of the graphics options. The MODEF command switches on the fastest,
but simplest, graphics mode. MODES, MODEC, MODEP make the graphics
options progressively more elaborate:
MODEF X11 only: switch on fast graphics mode;
MODES X11 only: switch on slabbing;
MODEC X11 only: switch on depth cueing (MODEC is the default)
MODEP X11 only: switch on perspective view (presently bugged)
These options all include the options above them in the list, so MODEP
also activates depth cueing and slabbing, for example. The default mode is MODEC.
See also the GRAFIC chapter.
See under MODEF above.
See also the GRAFIC chapter.
See under MODEF above.
See also the GRAFIC chapter.
This is the default grafics mode, i.e., when you do not use any MODE* command
WHAT IF behaves as if MODEC was given.
See under MODEF above.
See also the GRAFIC chapter.
This option presently is bugged.
The command RENUMB makes WHAT IF prompt you for a residue range.
It will then prompt you for the number to be given to the first residue
in this range, and will then renumber the residues in the
given range, using an increment of one.
One often wants to use WHAT IF for looking quickly at a structure.
It may be irritating to have to type the complete MOL-object number and MOL-item name
every time. The command SIMPLE will make WHAT IF choose
MOL-object numbers and MOL-item names automatically for every
MOL-item you generate.
The first item will be called A and put in MOL-object 1. The second one will be called B and
put in MOL-object 2, and so on. But after 8 items, WHAT IF starts
to prompt you for object numbers and item names again.
Use SIMPLE to toggle this option on/off, or SMPLON to switch it on,
and SMPLOF to switch it off.
The TRAROT command makes WHAT IF prompt you for a translation vector,
a rotation axis and a rotation angle. It will then show you the transformation
to be applied. It will ask you for a residue range,
and apply the transformation to that range. If you only want a translation,
set the rotation angle to zero.
The debug option SHOBUT will show the status of the 36 pickable
boxes (so-called buttons) at the bottom of the graphics window.
T means active (yellow) and F means inactive (white).
The debug option SHOIRF will show the status of the graphics flags.
These flags get their initial value from the last
line of the file WHATIF.FIG. (See the installation notes.)
The TOGGLI command will prompt you for the number of a graphics flag, and
will then toggle that flag from FALSE to TRUE or vice versa.
If you don't know what you are doing, don't do it with the TOGGLI
options - they can easily hang your system!
This is a debug option that you should not use.
This debug option lists which FORTRAN units are currently open,
and which files are attached to those units.
If you are afraid that some complicated option has corrupted the
soup, try the MOL200 option. It does not take much time, and when it gives no
output, WHAT IF thinks that
its soup is still OK. But if it gives ANY output, you are probably in trouble.
In this case your best bet is to use the MAKMOL command (see the
SOUP menu), terminate WHAT IF (with FULLST), check the PDB file that you made
with MAKMOL, correct this PDB file as necessary, and restart WHAT IF.
The WHAT IF commands can be divided into several categories.
The general commands are the ones that are always active: most of them are
described in the introduction (chapters
1-3). The so-called hidden commands, which are undocumented, but
nonetheless sometimes useful, and are described throughout this
writeup, as needed.
Many commands, however, are more logically grouped in menus. The following is a list
of some of the titles of chapters in this writeup that deal with one of
the more frequently used menus.
Surface area calculations (ACCESS)
Water operations (WATER)
Quality control (QUALTY)
Hydrogen bonds (HBONDS)
Contact analysis (ANACON)
Building proteins (BUILD)
Superimposing structures (SUPPOS)
Van der Waals menu (SETVDW)
NMR specific options (NMR)
X-ray specific options (XRAY)
Families and clusters (CLUFAM)
Data spreadsheet (TABLES)
Torsion-angle evaluation and manipulation (CHIANG)
Structure verification (CHECK)
Hssp-related commands (HSSP)
Secondary structure (DSSP)
Working with maps (MAP)
Symmetry operations (SYMTRY)
Amino acid structure regularisation (REFINE)
The electrostatics menu (ELECTR)
The structure fragment database (DGLOOP)
Relational protein structure database (SCAN3D)
Atomic parameter correlation rows (SEARCH)
Sequence manipulation (WALIGN)
Using the graphics (GRAFIC)
Graphics objects and items (ITMADM)
2-dimensional graphics (GRATWO)
Graphics enhancement options (GRAEXT)
Colouring atoms, residues, molecules, etc. (COLOUR)
Plotting (PLOTIT)
Labelling atoms (LABEL)
Working with GROMACS (GROMAC)
To go to a menu you have to type its name. Such names
are general commands, and therefore you can always go from any menu
to any other. Whenever you are in a certain menu, you can use the
END command to leave that menu.
The first couple of exercises in the tutorial will familiarise you with
travelling between the menus.
The menu bar at the top of the screen
holds the names of WHAT IF menus. Pick one of them
and a pull-down menu with most of the commands that you expect in this menu
will appear. Pick an option in this pull-down menu, and a window will
pop up. In this window you are already in the option that you picked. You do
not have to navigate through the WHAT IF menu maze first. The last line you
see in this pop-up terminal window is often: Hit RETURN to continue.
If you do hit return, the window disappears.
If you pick HELP in the right-most menu (right-most column, which
is always there) the HELP option will be activated.
If the HELP option is activated after you picked the
the pull-down menu box (which is green now),
you will get SHORT help on all the commands in this menu. But if the HELP option
is activated before you pick a box in the pull-down menu, the terminal window
will pop up, and extensive help about this option will be displayed.
The HELP option stays active until you pick HELP again.
There are many more pull-down menus than can be made visible at the same time.
At the time of writing (1 Mar 1994) there are some 50 pull-down menus.
The arrow buttons -> and <- left and right of the pull-down menus
can be used to scan through the pull-down menus in the indicated directions.
The GENMEN menu is redundant. All options available
in this menu are always active, whichever menu you are in.
But by going to the GENMEN menu, you can get a summary of
the options available, and you can get HELP, INFO, etc.
WHAT IF creates pictures in the graphics window, and puts text output in the
text window. All text sent to the text window can be written to a log
file. All pictures can be written to plot files in a wide variety of
formats. See the chapter on `WHAT IF output' for more details.
The command DOLOG opens the log file. All text written to the
text window after DOLOG will also be written to a log file.
See the chapter on `WHAT IF output' for more details.
After the command NOLOG, WHAT IF will stop writing text to the log file.
See the chapter on `WHAT IF output' for more details.
You can send commands to the operating system by preceding them with a dollar.
For example:
$ls /home/user/xdir
will (on a UNIX box) list the contents of the directory /home/user/xdir.
A small set of UNIX and UNIX-like commands have been hard-coded for
WHAT IF under UNIX. These are:
WHAT IF UNIX
LS ls
DIR ls
CAT more
TYPE more
RM rm
DEL rm
PWD pwd
Any text added after the WHAT IF command will be passed on to the UNIX machine.
That means that these options do NOT allow for type-ahead. E.g.:
LS LISTA 3
will result in the UNIX error message:
$ls lista
ls: lista: No such file or directory
WHAT IF normally ends with a remarkable quote or a silly joke.
If you are old and stuffy, or bored with all those jokes, you can put the
command NOJOKE in your startup file. That eliminates the jokes.
The jokes will be refreshed/extended automagically every so many months...
This chapter was last updated on 10-Jul-2006