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 reside in the main menu that you see in the
text window when you just hit RETURN. Several others reside in
the menu called GENOPT. These are the less often used options that
are potentially useful no matter in which menu you are presently working.
Despite that they reside in another menu, you dont have to go
to that menu to run the options. They are always active. You
have to go to BIGMEN, however, if you want to get help or short for
BIGMEN options, and automatic input command correction will only
work when you really are in the BIGMEN menu.
The WHAT IF main menu looks roughly like:
HELP INFO SHELL GENMEN END $.. %.. !.. SCRIPT
DOLOG NOLOG GO FULLST LISTA LISTR HISTOR GETMOL
GRAFIC GRATWO GRAEXT COLOUR PLOTIT PORNO ITMADM LABEL
SOUP 3SSP ACCESS ANACON BUILD CHECK CHIANG CLUFAM
DGLOOP DIGIT DOSELF DRUG DSSP ELECTR EXTRA HBONDS
HSSP MAP NEURAL NMR NOTES OTHER QUALTY REFINE
SCAN3D SCNSTS SEARCH SELECT SEQ3D SETPAR SETVDW SHAKE
SHOENT SPCIAL SUPPOS SYMTRY TABLES WALIGN WATER XRAY
GROMOS ANATRA ESSDYN TRAMOV CONOLY GRID
The top two lines holds the help and option control related options
HELP HELP gives help about option
INFO HELP gives extensive help about option
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 neath way
LISTA Lists atoms for (a range of) residue(s)
LISTR Lists the residues in the soup
HISTOR Show the options you recently executed
GETMOL Reads a PDB file
The third line holds the graphics related options:
GRAFIC Brings you to general menu to use the graphics window
GRATWO Brings you to menu to do two dimensional graphics
GRAEXT Brings you to menu for fancy graphics
COLOUR Brings you to menu to colour atoms/residues
PLOTIT Brings you to the menu from which to make plots
PORNO Brings you to the menu from which to use the sexy graphics options
ITMADM Brings you to the menu for the administration of MOL-objects/items
LABEL Brings you to the atomic labeling menu
The next all bring you to another menu. Soup is the most important
menu. The rest is given alphabetically:
SOUP Brings you to soup manipulation menu
3SSP Brings you to the 'superpose on all' menu
ACCESS Brings you to menu for accessibility calculations
ANACON Brings you in the contact analysis menu
BUILD Brings you to the residue building menu
CHECK Brings you to the structure validation menu
CHIANG Brings you to torsion-angle menu
CLUFAM Brings you in the clusters and families menu
DGLOOP Brings you to 3d fragment database menu
DIGIT Allows you to regenerate coordinates from stereo figures
DOSELF Allows you to do WHAT IF management things (write help, etc)
DRUG Brings you to the drug-design, docking, FLEXX interface, menu
DSSP Brings you to the menu to work with DSSP (or its emulator)
ELECTR Brings you to the menu to work with DelPhi (electrostatics)
EXTRA Brings you to a menu that does some other funny things
HBONDS Brings you in the hydrogen bonds menu
HSSP Brings you in the menu to work with HSSP files
MAP Brings you to map handling menu
NEURAL Brings you to the neural network toy menu
NMR Brings you to the NMR menu
NOTES Brings you to menu to make notes
OTHER Brings you to the yet another menu that does funny things
QUALTY Brings you to the quality control menu
REFINE Brings you to amino acid refinement menu
SCAN3D Activates the realtional protein database module
SCNSTS Allows you to do statistics on SCAN3D and DGLOOP groups
SEARCH Brings you to menu to search in the soup
SELECT Brings you to the menu to select proteins for SCAN3D
SEQ3D Brings you to the menu to regenerate the internal database
SETPAR Brings you in the menu to change parameters
SETVDW Brings you in the Van der Waals radius menu
SHAKE Brings you to the menu to build molecules ab-initio
SHOENT Brings you to the menu to look at the internal database
SPCIAL Brings you to the 'special' menu (undocumented options)
SUPPOS Brings you to the superposition menu
SYMTRY Brings you to menu to work with symmetry
TABLES Brings you in the spread sheet menu
WALIGN Brings you to the menu to work with sequences
WATER Brings you to menu to work with water molecules
XRAY Brings you to the menu with xray options
GROMOS Brings you to menu to work with the GROMOS EM/MD program
ANATRA Brings you in the trajectory analysis menu
ESSDYN Brings you to the essential dynamics menu
TRAMOV Brings you to the MD trajectory movie menu
CONOLY Brings you to the Connolly software interface menu
GRID Brings you to menu to work with Goodford's GRID program
The options to read coordinates should actually recide in the SOUP menu,
and that is also where they are described. However, these options are
so important that we decided to make several of them general options. I.e. you
can run them, no matter in which menu you are presently working.
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 fro the file name. You can
type the name of any PDB file. Include the path in the name, unless the file
resides 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 have to type
the .pdb or .brk extension to the file name.
After the file is found, you are prompted for the set name. Here all is
allowed. If you just give return, the set name will be the same as the file
name, and that is what you want in most cases.
If you ask for a PDB file by giving its PDB-assigned four letter code, and
that file does not exist on your system, WHAT IF will automagically get that
file from swift.EMBL-Heidelberg.DE, dump it in your local directory, and read it.
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 this
file will be read using the GETMOL command. See the NMR chapter for
more details.
The command GETGRO is similar to GETMOL (see above). With GETGRO however
one does not read a PDB file but a file in GROMOS format. see also the SOUP
chapter.
The command START will read a small molecule (crambin) without the need to know
where the PDB files are stored. START obtains this molecule from the
WHAT IF internal database.
The command DEMOS starts a 15 minute demo movie. This is not a pre-stored
movie, but a series of WHAT IF options calculated in a row.
WHAT IF allows you at all times to inspect the presently available sequence
information and coordinates. Both for the molecule(s) you are working
on as for all molecules in the database.
We separate three sets of options:
1) Looking in the database.
2) Looking at sequences.
3) Inspecting the molecule(s) you are presently working on.
The command LISTR causes WHAT IF to show you the entire amino acid
sequence. Depending on
the parameters (see the chapter on parameters) you get the sequence in one-
or three- letter code, optionally the amino acid frequency distribution and
the amino acid neighbor matrix are shown for proteins.
(See the chapter on parameter
setting for that, the default is showing only the sequence).
The command LISTRR will, when given,
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 Brookhaven file.
The command LISTA can be used to look at atoms, grouped per residue. WHAT IF
will prompt you for a residue range, and will then show for every requested
residue both the amino acid information like name, type, etc. and the atomic
information like coordinates, B-factor, Van der Waals radius, color (if
already set), charges (if already calculated) etc. This option also works
on drugs, water, etc.
Remember that you can use control/O (character O) to skip output to the
terminal in case you
accidentally asked for too much output.
The command LISTAA functions similar to LISTA, the difference being that LISTA
prompts you for one range of residues, waters, drugs, etc. LISTAA will prompt
you for multiple ranges (as usual, give 0 (zero) after providing all
ranges of interest).
Sometimes one wants to find the location of a sequence pattern, e.g.
Arg-Gly-Asp in a very big structure. The SHOPAT option can aid with
this. SHOPAT prompts you for three residue types (you can give
multiple types at each position). For every occurence of the pattern
the first position will be listed.
The sidechains of all observed patterns will be displayed.
You always have to give pattersn 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 occurence of your dipeptide pattern at the
C-terminus will remain undetected.
The command APROPO can only be used if Mosaic exists on your system, and
is callable with the command `Mosaic`. It will bring the WHAT IF
documentation in hypertext format in a Mosaic window. This is always
the latest version of the writeup (which resides on my machine) and
not necessarily the writeup that corresponds to your version on
your machine.
The command AUTOON will cause WHAT IF to create a (new) file SCRIPT.FIL. All
commands you give to WHAT IF are written in this file. After some minimal
editing
this file can be used as a script file for the SCRIPT option. (See also the
AUTOOF and SCRIPT options).
The command AUTOON will cause WHAT IF to log your commands in SCRIPT.FIL.
(See AUTOON). The command AUTOOF will close this file. Thereafter you should
edit this file as at present it will not (yet) automatically become a valid
script file (See command SCRIPT in the writeup).
The command DOLOG will cause WHAT IF to prompt you for the name of a log-file,
and for a comment to be written in this file. Thereafter all relevant
information that is written to the terminal/text-window will also be
written in this file. (See also NOLOG). (See also the chapter on logging
in the writeup).
The command DOLOG will cause WHAT IF to prompt you for the name of a log-file.
(See DOLOG). The command NOLOG will close this file. Thereafter you can
for example print the file with any valid print command preceded with a
dollar. (See also the chapter on logging
in the writeup).
The command HISTOR will show most of the main commands you recently
executed. Often also the main results or the parameters you gave the option are
listed. Not all commands are logged yet. (See also the chapter on logging
in the writeup).
The command SHELL will create a subprocess (on DOS as
well as on UNIX machines!).
In this subprocess you can do every normal thing you would
otherwise be able to do. However, due to memory requirements
you can not run big jobs. Also you can not run WHAT IF itself from such
a subprocess. You return from a subprocess into WHAT IF by typing exit.
You then get back into WHAT IF exactly at the location where you left it, and
not a single parameter has changed.
The command INFO 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, and you will get
the introduction paragraph of the chapter that holds the command XXX, and
the paragraph that deals with the command XXX itself at the terminal.
The command HELP can be used to get a limited amount of
help for a certain 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 at the terminal.
The command SHORT will cause WHAT IF to show you a list of all the commands
available in the menu you are in at that moment, followed by a description
in a few words of what that option can do for you. SHORT is now
implemented in almost all menus.
The command MAN-K (UNIX users can also type man -k) can be used to search
for all SHORT help lines with a certain keyword in it. 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.
The menu in which the command for which the SHORT line sits
given for each entry.
The command FIND can be used to get help for an option that is not in the
present menu. Just type:
FIND XXX
in which XXX stands for any option, and you will get
some help for the command XXX at the terminal.
The command SHORTT (with two Ts) gives short help about general options.
The option NOVICE toggles on the mode in which you automatically get
the HELP presented for every option that you use. As the name suggests,
this option is meant for novice users.
If you want to execute a DOS/UNIX command, you can first give the
SHELL command
in WHAT IF, and then do what you want to do in the spawned sub-process. If
you only want to execute one single command, it might be easier to just
type this command preceded by a dollar sign. WHAT IF will strip the leading
dollar character 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 in
WHAT IF.
If you know that a command exists, but forgot in which menu it sits, or do
not want to go to that menu first, you can execute it anyway by prefixing
it with a procent sign. E.g. %SHOSOU when given in the GRAFIC menu will
list the present contents of the soup.
The command NEWMOD will activate all options that are added in WHAT IF for
the next major release, but that are not yet fully tested and documented.
The command OLDMOD will de-activate all options that you activated with the
NEWMOD command.
The command DUTCH will force WHAT IF to talk Dutch with you.
As not always all messages got translated, WHAT IF will sometimes
talk one or two sentences English, but almost all will be Dutch.
WHAT IF's Dutch is sometimes a bit funny. That is because a large
fraction of the program messages got translated by WHAT IF itself...
The command ENGLISH will force WHAT IF to talk English with you. This
option, of course, only is useful if you changed the default language
earlier in the session. English is always the default language that
WHAT IF starts the session with.
The command FRENCH will one day force WHAT IF to talk French with you.
For now, only the prompt becomes French.
The command SPANIS will one day force WHAT IF to talk Spanish with you.
For now, only the prompt becomes Spanish.
At many places in WHAT IF parameters like line-thickness, number of dots
per sphere, radius of water, cutoff radius for distance calculations, etc.
seem somewhat arbitrary. I spend a lot of time thinking about good default
values, but if you nevertheless disagree with my choices, you can go into
the parameter setting menu with the SETPAR command. The parameter menu
has many parameter menus in it.
Many menus know the PARAMS command which brings you into the menu
to modify the parameters specific for that menu. A few parameters
function all over WHAT IF, and thus are hard to place in any
particular PARAMS menu. Those parameters are stored in the general
parameter menu that you enter with the command SETPAR.
The following commands are found in the 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 50% of the options
in WHAT IF that produce sequence output listen to this flag, the other
options do just 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 upon reading there is no B-factor
given in the coordinate file, and upon 'dreaming up' new atoms.
Do/don't use inter chain cys-cys bridges.
Use covalent neighbours in BUMP/CONTAC like options or not.
At many places in WHAT IF parameters like line-thickness, number of dots
per sphere, radius of water, cutoff radius for distance calculations, etc.
seem somewhat arbitrary. I spend a lot of time thinking about good default
values. If you nevertheless disagree with my choices, you can from many
menus directly go into 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 thus numbered. The file PARAMS.FIG (in the
dbdata directory)
holds the initial values for these parameters. You can poke new
parameter values directly into these parameters with the SETWIF
command. It is highly recommended that you do not use this option
unless you get desperate. SETWIF does not do any checking on
your parameters. Setting incorrect values with SETWIF can lead
to a program crash.
The command SHOWIF will prompt you for the number of a parameter
(see SETWIF). It will then show the documentation for
this program parameter.
The command MUTATE allows you to mutate residues. You will be prompted for
the number of the residue(s) to be changed, and subsequently for the
new residue type (give ala, cys, asp, etc). The new residue will be
placed in the molecule with plausible torsion angles, but without considering
bumps with other atoms. You are suggested to also look at the DGMUT, DGROTA
and the DEBUMP option. You are asked if you want to use "the experimental
version". Answer YES if you want the best new coordinates that WAHT IF can
think of. Answer NO if you intend to do the final touches by hand anyway.
(answering YES will cost you some time).
The command MUTZON causes WHAT IF to prompt you for a residue range and
a new residue type, just like MUTATE does. However, MUTZON will mutate
all residues in that range to one and the same residue type, rather than
prompting you for the new type at each residue. This option is meant
for making poly-alanine, or poly-glycine etc chains.
Normally WHAT IF will refuse to mutate residues to the same type that
they already are. If you want to see what WHAT IF thinks about a tryptophan
at position 17, but there already sits a tryptophan at that position, you can
of course first mutate it into an alanine, and thereafter ask WHAT IF to
make it a tryptophan again for you. For this special case you can use the
MUTSLF option as a shortcut. MUTSLF will do just the above described
mutation scenario (of mutating to and back from alanine) for you.
The option SUGMUT will cause WHAT IF to prompt you for residue
ranges. For every residue in this range it will try all 20
amino acids and give them a score. The highest score is printed.
I have no idea how to interpret the score, but it looks as if a
clearly positive score means that the protein will still fold
whit that mutation in it. Please carefully inspect things afterwards
yourself. This option does not take into account: symmetry contacts,
crystal waters, the active site and ligands.
This option is a bit time consuming.
The option TRYMUT does virtually the same as SUGMUT. However, rather
than leaving the molecule unaltered and merely telling you what
it thinks would be smart mutations to make, this option actually
makes what it thinks are smart mutations. You will be prompted for
a 'number of cycles'. That is because once a mutation is made, other
residues will see another environment, and might need another
residue type at to be optimal.
This option is a bit time consuming.
If you have made a mutation, or for any other reason a residue is placed
such that its side chain atoms have too close contacts with other residues,
you can use the DEBUMP option. DEBUMP will prompt you for the number of
steps. This number of steps is divided on 360 degrees, and the outcome is
the step size in degrees by which every free rotatable side chain chi angle
will be rotated in order to find a conformation with less overlap with
neighboring residues. If you do not want to change the degree of
staggered-ness or eclipsed-ness, you should of course give 3 for the number
of steps, because then every combination of the rotation of every chi-angle
with 120 degrees will be tried.
Please remember that some residues have 4 freely rotatable torsion angles in
their side chain. Debumping these with 10 steps per torsion angle will cost
10000 bump analysis, and that can be more CPU time than you intended....
If you have made a mutation near the protein surface, just debumping is
often not enough because there is infinite space where the side chain can
sit without bumps. In such a case you would actually like to do a single
residue energy minimization. It is our experience that a DEBUMP run with
parallel search for hydrogen bonds works normally equally well. The option
DEBHBO does the same as DEBUMP, but additionally scores for hydrogen bonds.
The hidden command DEBALL can be used to run one round of debumping over a
range of
amino acids in the SOUP. (See DEBUMP for information). You can either
give a range of residues to be DEBUMP-ed or you can give a file with the
original residue names (those listed by WHAT IF between
brackets). If a file DEBUMP.LIST is present, that file will
automatically be used. The file format is
- one line with the number of residues to be debumped
- per residue one line with its original name.
The first residue found in the file will be debumped first etc.
The hidden command DEBTRS can be used to run one round of translational
debumping over a range of
amino acids in the SOUP. All residues will be translated by +/- 0.1 Angstrom
in the X, Y and Z direction. The situation with the fewest bumps will be
kept. It is highly recommended to use the REFI option in the REFINE menu
afterwards.
The command IUKKEL will cause WHAT IF to automatically activate the option
SAVSOU (see the SOUP chapter) every 10 options that you execute.
WHAT IF allows you to rename commands. Start a command with the > sign,
followed by a real command. Continue on the same line with a > sign again
followed by the new name for this command. This way you renamed one command.
If you want to use this new command name, start the command with
the < sign and follow it by the new command name.
Example:
>LISTA >TYPE ATOMS to rename the LISTA command
<TYPE ATOMS to use the new command
The new command can only be used in the menu where the original command
resided. You can only rename 100 commands. Since renamed commands will
not be remembered by WHAT IF from the one to the other session, it
is advised to make a SCRIPT file for them.
You can use the command >> (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 that started with this character(s) will be repeated.
You can use the hidden command .P (period,P) to get a list of the last
one hundred 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 that started with this character(s) will be repeated.
You can use the hidden command .P (period,P) to get a list of the last
one hundred commands. Instead of a period you can
also use an exclamation mark (!).
For the command > see under the command <.
The command MAKSCR normally is rather useless, but it is needed for running
the tutorial (see the tutorial chapter).
The SCRIPT option can be used to play a script of pre-typed commands.
This option is extensively described in a separate chapter called
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 pre-typed commands over
a set of PDB files.
This option is extensively described in a separate chapter called
SCRIPT FILES. You are urged to read this chapter first, because LSCRIP
is a bit tricky.
The command TEACH is the obligatory first command in any teaching script.
(See the chapter on teaching scripts; and see
http://swift.embl-heidelberg.de/workshop/ for more info).
After you used one of the menu commands 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....
After you used several of the menu commands you go one menu down
in the menu tree.
You can go back to the menu you came from with the END command, but you
can go back all the way down till the first menu with the QUIT command.
The command FULLSTOP (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 a normal state, so that it is useful for the next user.
Especially at 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 empty menu build in. You cam use this menu to write your
own options, without having to worry about the menu level administration,
or the creation of pull-down menus. The command MYMENU brings you in
this menu. See the EXTRA menu.
The command MORE shows up in some 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 command is to let the
user concentrate on the most important options.
The command LESS reverses the action by 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.
Wit GO you pass control from the text window to the graphics window.
In the graphics window you pick CHAT to get back in the text window again.
The command EDT will prompt you for a file name, and it will get this file
in the editor. The editor that is chosen is determined by the editor record
in the CCONFI.FIG file. You decided what your favourite editor is upon
WHAT IF installation, 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.
The command ANGLE3 will three times prompt you for a residue and
an atom in this
residue. First you will be prompted for the middle residue/atom, thereafter
for the residue/atom 1 and 2. It will calculate the angle from atom 1 over
the middle atom to atom 2.
The command DIST will twice prompt you for a residue and an atom in this
residue. It will calculate the distance between these two atoms.
Normally WHAT IF does its graphics via MOL-objects and MOL-items. After the
command DIRECT however, molecules, residues and atoms are always updated
directly if modified. Other graphics like e.g. H-bonds are still put into
MOL-items. This option resides in the GRAFIC menu, but can be activated from
every menu.
See the GRAFIC menu.
When you interactively inspect interatomic distances WHAT IF will draw a line
between the two atoms, and write the interatomic distance at the midpoint
of this line. This line, and the distances will be updated continuously. The
option DSTOFF will selectively remove all lines and distances from the
screen, and will terminate their continuous update. Clicking NOID in the
graphics window once, will do the same, but will additionally remove several other
interactive graphics items from the screen (i.e. NAYB, simple interatomic lines,
etc).
The command MINMAX will cause WHAT IF to prompt you for a residue range.
It will then determine the extreme values for the coordinates in this
range. It will also determine the center of gravity of this range. You will
then be asked if you want to center the SOUP. If you answer YES, the
whole SOUP will get new coordinates, such that the center of gravity of
the given range will become 0, 0, 0.
The command SHOCEL will cause WHAT IF to list all kinds of cell-dimension
information. The cell as read from the PDB file is listed together
with the cell that can be reconstructed from the PDB SCALE records.
Additionally, WHAT IF uses artificial cell dimensions from GRID maps, DelPhi
maps, surface maps, etc. SHOCEL will also summarise the cell artificial
dimensions that come with those maps.
The main menu has several so-called hidden commands.
The command CENXYZ will cause WHAT IF to prompt you for the coordinates
of a point in space. This point will be the new center of the graphics
screen. Nothing happens if you do not yet have an active graphics window.
The command CHESS will start a 1100 ELO rating chess program. (At least, if
you activated it upon WHAT IF installation).
The command CHOOSE will prompt you for ranges. Every next command
that normally prompts you for multiple ranges will now no longer
ask for ranges, but use those you gave after the CHOOSE command.
Use the command CHOOSE again to select new ranges.
Use NEWRNG to de-activate the ranges set with CHOOSE. After NEWRNG
WHAT IF will prompt you again every time ranges are requested.
Options that only require one residue or one single range of residues
as input are not affected by the CHOOSE and NEWRNG commands.
The command FOOOOD will cause WHAT IF to tell you time and date.
This information can be combined with the sounds from your stomage to
determine if it is getting time to eat some food.
The more serious equivalent of FOOOOD is TIME. This option can even be used
from the graphics window.
Several WHAT IF options will get files in the editor. Which editor
that is, is determined by your choice upon WHAT IF installation.
The default editor is indicated in the file CCONFI.FIG.
The command SETEDT allows you to get another default editor
for the duration of this WHAT IF run. Please make sure you only
use editors that stop the WHAT IF execution while the editor is
active (or give the editor some flags to create this behaviour).
If you dont do this, there is no sense in getting input parameters
for a program in the editor for inspection and correction, because
that program would already be running with the default parameters
by the time you close the edit session.
On X11 systems only you can (at the cost of rotation speed) increase the level
of sophistication of the graphics options. The MODEF command switches on the fastest, but most primitive
fastest and simplest graphics mode. MODES, MODEC, MODEP make the graphics
options progressively more sophisticated:
MODEF X11 only: switch on fast graphics mode
MODES X11 only: switch on slabbing
MODEC X11 only: switch on depth cueing
MODEP X11 only: switch on perspective view
These options all include the options above them in the list. So, MODEP
also activates depth cueing and slabbing. 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.
See under MODEF above.
See also the GRAFIC chapter.
The command NEWRNG will de-activate the automatic ranges set with
the CHOOSE command.
The command RENUMB will cause WHAT IF to prompt you for a residue range.
It will thereafter prompt you for the number to be given to the first residue
in this range. It will then renumber the original residue names of the
given range, starting from the first one, and using an increment of one.
Often one wants to use WHAT IF for quickly looking at a structure. In those cases it is not nice
that one needs to type the complete MOL-object number and MOL-item name
every time. The command SIMPLE will cause WHAT IF to decide itself
what the MOL-object number and the MOL-item name will be 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, etc. After 8 items were made this way, WHAT IF starts
again to prompt you for object numbers and item names.
Use SIMPLE to toggle this option on/off, or SMPLON to toggle it on,
and SMPLOF to toggle it off.
The command TRAROT will cause WHAT IF to 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,
you can give zero for the rotation angle.
The debug option SHOBUT will show the status of the 36 pickable
boxes, or so-called buttons, at the bottom of the graphical window.
T means active, or yellow; F means inactive or white.
The debug option SHOIRF will show the status of the so-called graphics flags.
These are the flags that get their initial value from the last
line of the file WHATIF.FIG. (See also the installation notes).
The command TOGGLI will prompt you for the number of a graphics flag.
It will change that flag from FALSE to TRUE or vice versa. Be aware that
if you dont know what you are doing, you should not do it with the TOGGLI
options. The TOGGLI options can easily hang up your system.
Debug options which you should not use.
This debug option lists which FORTRAN units are presently open,
and which files are attached to those units.
If you are afraid that some funny complicated option has corrupted the
soup, you can try the MOL200 option. This option does not take
any measurable time, and when it gives no output, WHAT IF thinks that
its soup is still OK. If it gives ANY output, you are most likely in trouble.
In that 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, optionally correct this PDB file and restart WHAT IF.
The SPCIAL menu holds very meny options that are not documented. Most
of these options were written for a friend, and sometimes you can guess
from the name of the option who that friend is.
In due time, we might write here a one or two line explanation
for each of these options. For now:
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
Flip sidechains of all Asn, Gln and His is soup. With this option
you can check the quality of the HB2NET routine in the HBONDS menu.
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
Still to be documented.
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Still to be documented.
When you are working in a menu, WHAT IF can correct the options
in that menu. To do so, it tries several heuristics:
1) The three letter code most used 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. In case of five character commands, both possible
swap combinations are tried.
3) All character O are replaced by digits zero or vice versa.
4) All characters I are replaced by digits 1 or vice versa.
5) All single character deletions, insertions and typos are tried
and each time the results are compared with all options in this
menu. If one single solution pops up, this one 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 options, this
swap is applied.
However, the above option correction only works for options that
are found in a menu. General options cannot be corrected.
As it is about as likely that a typo is made in a general option as
it is that a typo is made in an option in a menu, we wanted to do
something about the most likely typos in general options. The
list of options below are valid typos:
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.
Alternative spelling for GRAFIC and GRAPHIC.