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.
This chapter describes these options.
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.
The command GETMLS will prompt you for a file name. All PDB files listed in this
file will be read using the GETMOL command.
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.
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 GETDSP will prompt you for a DSSP file. The coordinates (alpha
carbons only) will be read from this file as if it was a PDB file holding
only alpha carbon coordinates.
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 does not show up in any menu, but it 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. LISTRR is a so-called hidden command (See HIDDEN COMMANDS).
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 to skip output to the terminal in case you
accidentally asked for too much output.
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. Not all commands are logged yet. See the chapter in the writeup
about logging and history logging.
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. It presently only works for
a few menus, but during 1995, it will be extended to most other
menus.
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.
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.
The SETPAR menu lets you enter a menu from which many parameter menus can
be activated. See PARAMS for a direct way of entering these menus.
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.
WHAT IF has the capability to run the program DSSP (written by Kabsch and
Sander, see the appendices for a further description and acknowledgments)
without you having to do anything than but typing SHOHST.
The DSSP determinations of
secondary structure are used by WHAT IF. If you do not know the DSSP
principles, I suggest you read the article, but in short: No code means random
coil; H means normal helix. 3 means 3-10 helix; T means turn, and
E mean extended. You can get the secondary structure determination by
typing SHOHST.
In case you don't have a DSSP lisence, WHAT IF will determine the secondary
structure itself. However, DSSP does this much better...
Since WHAT IF already knew about secondary structure before I knew about
DSSP, there is a renaming of secondary structure codes upon reading in.
DSSP-H,I -> WHAT IF-H
DSSP-G -> WHAT IF-3
DSSP-E -> WHAT IF-S
DSSP-B,T -> WHAT IF-T
DSSP-S is neglected by WHAT IF.
Sorry for this....
This command will list the sequence at the screen in one-letter code. It will
also for every amino acid show what its secondary structure is. If the
secondary structure has not been calculated yet, it will automatically
issue the call to DSSP first. This option evaluates secondary structure,
it will NOT predict it!
If you made some changes in the molecule, WHAT IF can not determine itself
if it is time to call DSSP again for a new secondary structure evaluation.
The command SHOHST will therefore display the old evaluation results. You
can force WHAT IF to call DSSP again with the command NEWHST followed
by SHOHST.
The hidden command ALLHEL will convert all secondary structure
values in H (helix). This option should be used after SHOHST. It only changes
what WHAT IF thinks that the structure looks like, and does not change anything
in the structure.
The hidden command EDTHST will cause WHAT IF to prompt you for a residue range.
For every residue in this range you will see the local sequence and secondary
structure determination. You will residue by residue be prompted for the
new secondary structure determination. This option should be used after the
SHOHST command.
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.
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.
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.
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 % can not 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 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.
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.
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.
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.
Many WHAT IF commands exist only to bring you in a certain menu. If you use
the pull-down menus, you will never need these commands. All these menus
have extensive help in them for their commands. Here only the main function of
the menus will be listed.
The command 3SSP brings you in the 3SSP menu. This menu holds all the options
to run the MOTIFS option (see SUPPOS menu) against the whole database. There
are also options to evaluate the results.
The command ANATRA brings you in the menu for molecular dynamics
trajectory analysis. At present GROMOS and CHARMM trajectories can be
analyzed. Movies can be shown, and WHAT IF scripts can be run over whole
trajectories.
The command ACCESS brings you in the menu her you can do solvent accessible
and Van der Waals surface calculations and evaluations.
The command ANACON brings you in the menu from which you can do all kinds
of atomic contact related commands.
Ab initio model building is impossible. The command build allows you just to
do that: the impossible.
The command CELADM will cause WHAT IF to activate the crystallographic
cell operation menu. At present this menu only holds one command:
The command SHOCEL will list the crystallographic cell dimensions
of the last read PDB file.
The command CHECK will cause WHAT IF to activate the protein structure
checking module. In this menu you have a multitude of options that all check
certain aspects of the quality of your protein.
The command CHIANG brings you in the torsion angle determination, evaluation
and manipulation menu.
The command CHKMDF brings you in the menu that allows for visual inspection
and interactive manipulation of H,K,L,F reflection files (provided they
are in the Groningen style MDF format).
The command CLUFAM will bring you in the cluster and family menu. There
is a separate chapter in the writeup (and in INFO) for this menu.
The command COLOUR brings you in the menu from which to color atoms, residues
or molecules. You can color by type, property, parameter correlation row,
mutability, spread sheet table, secondary structure, etc.
The command CONOLY brings you in the menu from which you can work with the
Connolly software (provided you have this package).
The command DGLOOP (called so in honor to Alwyn Jones who used the same name)
brings you in the WHAT IF distance geometry loop searching algorithm.
Here you can search for loops, but also construct whole models from just alpha
carbon coordinates.
The menu DRUG will one day contain many drug design options.
The menu EXTRA contains some options to aid with the determination of
of protein folding initiation sites. One day this menu will be documented.
The command ESSDYN brings you in the menu where essential dynamics related
options can be executed.
The command GROMOS brings you in the menu from which you can interface
to GROMOS (Molecular dynamics and energy minimization package).
There is a GROMOS pre-compiler that can make GROMOS input files for
some of the simpler GROMOS options like energy minimization in vacuum.
There is also is generalized small molecule topology maker that can create
the largest part of the PROxxx input decks needed to make topology files
for molecules for which there are no building blocks in the GROMOS data
files. (This topology maker was donated by Bauke van Eijck).
The command GRAFIC brings you in the main graphics menu.
This menu is well documented. (See chapter on GRAFIC).
The command GRAEXT brings you in one of the two menus for fancy graphics
options. (The other menu is the PORNO menu). In GRAEXT you will find some
small graphics enhancement options like spheres of dots around an atom,
arrows in 3D, etc. In PORNO you will find the REAL fancy stuff.
The command GRATWO brings you in the menu from which you can do two
dimensional graphics operations like pickable phi-psi plots, etc.
The command GRID brings you in the menu to interface to the GRIN GRID
potential energy calculation programs.
The command HBONDS brings you in the hydrogen bond calculation, display and
evaluation menu.
The command HYDMOM brings you to the menu from which you can do property
moment calculations such as hydrophobic moment calculations. This menu is
rather poverly documented, and far from bug free....
The command HSSP brings you in the menu from which you can manipulate HSSP
files.
The command ITMADM brings you in the menu that allows you to
manipulate (Toggle on/off, remove, delete, retrieve) MOL-items
and MOL-objects.
The command LABEL brings you to the menu where you can label atoms.
The old PS300 machines were too slow to continuously update the screen. To
at least allow the user to see what a mutated residue looked like, without
having to regenerate the entire picture at the screen the working model was
introduced. The residues stored in the working model show up in yellow.
On newer machines this menu is not needed, although, you should realize
that the command NOMODL that sits in the GRAPHIC menu can be used to get rid of
residues that show up as the result of mutations, FBRT, etc., options. Over
the next year or so, the working MODEL idea will be phased out.
The menu MAP holds all kinds of options to manipulate maps. Maps can be
crystallographic electron density maps, surface contour maps, or GRID potential
energy maps.
The command MASMAP brings you in the menu where you can massage electron
density map values (e.g. smoothing, spike removal, scaling, etc.)
The command MAPEDT activates an electron density envelope editor. Two maps
are required: a normal electron density map, and a map consisting of 1s and
0s only.
The command NEURAL brings you in the toy neural network menu of WHAT IF.
This menu does not hold a real good, fast neural network, but a small toy
network for playing purposes.
The command NOTES brings you in a notebook menu that allows you to make
general as well as residue specific notes.
The command PLOTIT brings you in the plot menu.
The option PORNO will bring you to the menu where the real fancy graphics
are done (molecular pornography menu). This menu holds an interface to
Mike Carson s RIBBONS program.
The command NMR brings you in the NMR menu of WHAT IF. This menu has several
NMR specific options in it, as well as many options that work on many
proteins at the same time.
The command PIRPSQ brings you to the old sequence manipulation menu.
From this menu you can do the model building by homology. WALIGN brings
you in the new, but not yet ready, sequence manipulation menu.
The command QUALTY brings you in the menu from which you can do protein
structure quality control based on packing contact normality.
The command REFINE brings you in the regularisation menu. Here you will find
the options to patch up your molecule after you did some manual modeling.
The command SUPPOS brings you in the menu to superpose proteins or co-factors.
This menu also holds the famous MOTIFS option. MOTIFS will fully
automatically superpose two proteins without any human intervention.
The command SETVDW brings you in the menu her you can modify the Van der Waals
radii of atoms. (useful option to calibrate programs...).
The command SCAN3D brings you to the menu from which you can access
the WHAT IF relational database module.
The command SEARCH brings you in the parameter correlation menu. In this menu
you can do searches like: "Where are the buried hydrogen bond donors that
are not involved in a hydrogen bond." etc.
The command SELECT brings you in the menu from which you can select the proteins
to be used by the SCAN3D options.
The command SEQ3D brings you in the menu from which you can create a
WHAT IF SCAN3D relational database. You better do not use this menu unless
you REALLY know what you are doing.
The SOUP command brings you in the SOUP menu. Here you can do soup
administration operations like reading in or deleting molecules, residues etc.
The command SPCIAL or SPECIAL will bring you in the special menu. This menu
holds some hundred options that were quick hacks to solve some problem
for a friend one day. These options are not documented, mostly bugged, and
they got cryptic names.
The command SYMTRY brings you in the symmetry operations menu.
The command TABLES brings you in a very primitive molecular
spread sheet menu. You can make tables with residue names, accessibilities,
packing qualities, etc. There are also some simple table comparison
and math operations.
The command WALIGN brings you in a menu where you can work with sequences
(alignment, reading, writing, database searches, etc). This menu has menu
sub-menus in it.
The command water brings you in the menu to manipulate bound water atoms.
The command XRAY brings you in a menu with Xray crystallographic options. Most
of these options also occur somewhere else in the program, but here they are
nicely concentrated to save the crystallographer a lot of menu navigation.
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.
The command CHARGE will set then charges for all atoms in all amino acids.
These charges are taken from a lookup table which
can be found in the database directory under the name CHARGES.PROT.
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 TRNSFM brings you in a menu where you can check/modify WHAT IF's
internal transformation matrices. This menu is not yet ready. It will be
useful mainly for crystallographers.
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.
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.
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 MODEF above.
See MODEF above.
See MODEF above.
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.
The command SETWIF prompts you for the number of a parameter, and a new
value for this parameter. You better know what you are doing if you use
this option.
Upon installation WHAT IF creates a couple configuration files. These
are called *CONFI.FIG where * is a character. These files hold parameters
like the colour of the text in menus etc. You can modify the file ICONFI.FIG
to change colours, etc. You can also change these parameters on the fly
with the SETICO command.
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 or off.
Debug options which you should not use.
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.