This menu holds several three dimensional graphical options that
are not used too often. Many of these options are meant to enhance
your graphics (e.g., arrows, displayin a wire-frame crytallographic
cell, cylinders through helices). Some of these options are a whole
little program in themselves.
The GRAEXT command shows more options than listed in this chapter. Those
undocumented options are most likely bugged.
The options logically separate in options that enhance the GRAFIC menu options;
options that generate simple objects; options that belong inbetween the GRAFIC
and ANACON menu; other, facy graphics, option.
The option GRAAA will cause WHAT IF to prompt you for a residue range.
Thereafter you can select residue types. WHAT IF will ask you to
give residue types, you should type all desired types at one line.
All residues of the given types in the given range will be put in a mol-item.
The option GRAAA will cause WHAT IF to prompt you for a residue range.
Thereafter you can select residue types. WHAT IF will ask you to
give residue types, you should type all desired types at one line.
The side chains of all residues of the given types in the given range will
be put in a MOL-item.
The command PLUTO will prompt you for a residue range. It will generate a
ball and stick model for this range. The balls are represented by dots at
their surface. The sticks are made of many parallel lines laying on a
cylinder between the connected spheres. Of course rather small atomic
radii are being used (default is 0.5 Angstrom). The atomic radii, the
thickness of the bonds, and the number of lines that make up a bond
can be changed with the parameter setting module. (See the chapter on
parameter setting). This is not a CPK picture, but a simple line
drawing. The dots and the sticks are stored in two
different mol-items, since WHAT IF objects do not allow for mixing them.
The command PLUTOS will prompt you for a residue range. It will generate a
ball and stick model for side chains of the residues in this range.
The balls are represented by dots at
their surface. The sticks are made of many parallel lines laying on a
cylinder between the connected spheres. Of course rather small atomic
radii are being used (default is 0.5 Angstrom). The atomic radii, the
thickness of the bonds, and the number of lines that make up a bond
can be changed with the parameter setting module. (See the chapter on
parameter setting). Since this is not a CPK picture, but a simple line
drawing. The dots and the sticks are stored in two
different mol-items, since WHAT IF objects do not allow for mixing them.
The command ICOATM will cause WHAT IF to prompt you for an atom in a
residue. A small icosahedron with the same radius as the spheres
drawn by the PLUTO and PLUTOS options will be drawn around this atom.
The command AXIS will draw a small axis system with its origin at the origin
of the graphics system. You will be prompted for the length, the number
of divisions (tick-marks) and the label at each of the three axes.
You will at the end be prompted for the origin of this system, this
will be the point where the three axes come together.
This command creates a wire frame box around your crystallographic cell.
This command creates a box around cells. You will be prompted for the order
of the cells. Order is 1 draws one cell just as the option CELL does. Order
is 2 draws
2*2*2 (is already eigth) cells. Order is 3 draws 3*3*3 (is 27) cells, etc.
The command LINATM will cause WHAT IF to prompt you twice for a residue and
an atom in that residue. A dashed line will be drawn between these two atoms.
The same effect can be obtained with the screen menu item LINE. However,
LINATM puts the line in a MOL-item, and that implies that the line can be
toggled on and off, can be plotted, etc.
The command DOTATM will cause WHAT IF to ask you for an atom. Around this
atom a dotted sphere with the Van der Waals radius as sphere radius will
be drawn.
The command arrow draws an arrow in three dimensions. The arrow points at
(0,0,0), but with the MOVITM command you can move the arrow around in space.
The size of the arrow is under parameter control.
The command BARROW will react in all aspects the same as the command ARROW
(see above), but it will make an arrow which contains of nine little cylinders
which together make a ninety degree bend arrow.
The command TARROW will react in all aspects the same as the command ARROW
(see above), but it will make an arrow which contains of ten
little cylinders
which together make a one hundred eigthy degree turned arrow.
The command HELLIN will cause WHAT IF to create lines that
best fit the central line through all helices in your structure.
Per helix you will be prompted whether this one should be drawn or not.
This option could crash WHAT IF. Make sure to save your work (e.g. with
the SAVSTA command) before you run this option.
The command HELCYL will cause WHAT IF to create cylinders that
best fit the backbone of all helices in your structure. Per helix you will
be prompted whether this one should be drawn or not.
This option could crash WHAT IF. Make sure to save your work (e.g. with
the SAVSTA command) before you run this option.
The command HELCA will cause WHAT IF to prompt you for a residue range. It
will than create cylinders that
best fit the backbone of all helices in this range.
For the non-helical stretches in the given range a normal alpha carbon trace
is drawn.
This option could crash WHAT IF. Make sure to save your work (e.g. with
the SAVSTA command) before you run this option.
The command CONCHG will cause WHAT IF to ask you to pick an atom. Thereafter
you will be prompted for a range of residues. Dotted lines will now be drawn
between the picked atom and all acidic and basic atoms in the
direct environment. You will be askes for a cutoff value which is the
upper limit of the interatomic distance that you consider acceptable.
You will also be asked if histidine should be considered
basic or not. If yes answer this question with YES, both histidine side chain
nitrogens in all histidines will be treated as basic.
The command CATSCP will prompt you for a residue range and a contact distance.
An alpha carbon trace will be drawn for the range. Lines will be drawn
between alpha carbons of residues that make a contact. A residue pair
that has at least one pair of contacting atoms (that means that their
Van der Waals
surfaces are less than the given distance apart) is called in contact.
The connecting lines are called as colour of the number of residues contacted
by the entire residue. Contacts to direct covalently bound neighbours in the
sequence are skipped.
This is a nice option to quickly get an impression about which residues
are important, and which residues are not.
The command LINFIL allows you to read graphics lines from a file. The lines
have to be written one graphics line per line in the input file. The format is
7(F10.0,1X), that means 7 real numbers that are written in the colums 1-10,
12-21, 23-32, etc. The position of the decimal point within the numbers is free.
The first three numbers are the X, Y and Z coordinates of the one end of the
line. The 4-th till 6-th number are de coordinates of the endpoint. The seventh
number is the colour on the usual 0 - 360 scale.
The command DOTFIL allows you to read graphics dots from a file. The dots
have to be written one dot per line in the input file. The format is
4(F10.0,1X), that means 4 real numbers that are written in the colums 1-10,
12-21, 23-32, and 34-43. The position of the decimal point within the numbers
is free.
The first three numbers are the X, Y and Z coordinates of the dot. The fourth
number is the colour of the dot on the usual 0 - 360 scale.
The command ALLFIL allows you to read graphics lines, dots, labels and viewing
directives from a file. This file is keyword driven. That means that every line
starts with a keyword. Allowed keywords are DOT, CROSS, LINE, DASH, CENTER, TEXT
(or LABEL), RESIDUE, CALPHA, CONE, CIRCLE, WHEEL, BALL and END.
The ALLFIL command can be preceded by the SIMPLE command. This ensures that
WHAT IF will for up to eight MOL-items not prompt you for anything. Give
SIMPLE again to disable the simple graphics mode.
WARNING. Be aware that if one of these options requires N input parameters
anything else than exactly N parameters will lead to errors. In other words
there is virtually no error checking done on ALLFIL files.
You can cut the next file from the writeup and feed it as input file to
the ALLFIL command.
DOT 2 2 2 RED
DOT 2.1 2 2 RED
DOT 2 2.1 2 RED
DOT 2 2 2.1 RED
DOT 2.1 2.1 2 RED
DOT 2.1 2 2.1 RED
DOT 2 2.1 2.1 RED
DOT 2.1 2.1 2.1 RED
DOT 8 2 2 RED
DOT 2 2 10 BLUE
DOT 7 2 10 BLUE
DOT 2 7 2 RED
DOT 7 7 2 RED
DOT 2 7 9 BLUE
DOT 7 7 9 BLUE
DOT ITEM
CROSS 1.2 2.2 3.6 BLUE
CROSS 2.2 2.2 3.6 RED
CROSS 3.2 2.2 3.6 GREEN
CROSS 4.2 2.2 3.6 YELLOW
CROSS 5.2 2.2 3.6 PURPLE
CROSS 6.2 2.2 3.6 CYAN
CROSS 7.2 2.2 3.6 MAGENTA
CROSS 8.2 2.2 3.6 ORANGE
CROSS ITEM
DASH 1 1 1 8 1 1 10
DASH 1 1 1 1 1 10 10
DASH 8 1 1 8 1 10 BLUE
DASH 1 1 10 8 1 10 BLUE
LINE 1 1 1 1 7 1 GREEN
LINE 8 1 1 8 7 1 GREEN
LINE 1 7 1 8 7 1 120
LINE 1 7 1 1 7 10 120
LINE 1 1 10 1 7 10 GREEN
LINE 1 7 10 8 7 10 GREEN
LINE 8 7 1 8 7 10 RED
LINE 8 1 10 8 7 10 RED
LINE ITEM
TEXT 8 1 10 CYAN
one corner point
TEXT 8 7 1 CYAN
another corner
ARROW 1.3 1.2 1.8 3.0 5 -6.1 RED
ARROW ITEM
PLANE 1 1 1 2 2 2 3 3 3 4 4 4 purple
CIRCLE -6 0 0 0 0 1 3 GREEN
WHEEL -6 0 0 0 0 2 3.5 3.7 260
RESIDUE 1 2
RESIDUE 4 5
CALPHA 6 10
RESIDUE ITEM
LINATOM 6 O 10 N red
BALL 6 CA
BALL 7 CA
BALL 8 CA
BALL ITEM
CONE 1 1 1 4 4 4 30 YELLOW
CONE ITEM
HAT 1 1 1 4 4 4 30 8 YELLOW
HAT 1 1 1 4.2 4.2 4.2 30 12 ORANGE
HAT ITEM
TRICONE 0 0 0 1 0 0 0 1 0 0 0 1 1.5 12 RED
TRICONE ITEM
CENTER 1 1 1
SCALE 0.6
END
All options in ALLFIL are closed with an ITEM command, this
is CONE ITEM for cones, LINE ITEM for lines, etc. However, you
do not need to close every option immediately with an ITEM command.
Multiple options that produce the same kind of data (lines or dots) can
be combined in one ITEM. So, the following ALLFIL file will work fine:
CROSS 7.2 2.2 3.6 MAGENTA
DASH 1 1 1 8 1 1 10
DASH 1 1 1 1 1 10 10
LINE 8 1 10 8 7 10 RED
ARROW 1.3 1.2 1.8 3.0 5 -6.1 RED
CALPHA 6 10
RESIDUE ITEM
DOT 2 2 10 BLUE
DOT 7 2 10 BLUE
BALL 7 CA
BALL 8 CA
BALL ITEM
The following groups of commands are allowed to reside in one ITEM:
MOLLAB
LINE DASH ARROW CROSS CONE HAT PLANE RESIDUE CALPHA CIRCLE WHEEL TRICONE
BALL DOT
I.e. You can have LINE and CIRCLE in one ITEM, but not LINE and BALL, nor
WHEEL and MOLLAB, etc.
The following commands are independent commands that do not sit in ITEMs:
CENTER
LABEL/TEXT
SCALE
The LINE command has the format:
LINE 7 numbers (or 6 numbers and a colour)
The first six numbers are X,Y,Z of the begin and end point of the line.
There should either be a seventh number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of LINE commands should be closed with the LINE ITEM command.
The ARROW command has the format:
LINE 7 numbers (or 6 numbers and a colour)
The first six numbers are X,Y,Z of the begin and end point of the arrow.
There should either be a seventh number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of ARROW commands should be closed with the ARROW ITEM command.
The CIRCLE command has the format:
LINE 8 numbers (or 7 numbers and a colour)
The first three numbers are X,Y,Z of the center of the circle.
The second three numbers for a vector orthogonal to the circle. Make sure
that these first two vectors do not fall on one line with the origin!
The seventh number is the radius of the circle.
There should either be a eighth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of CIRCLE commands should be closed with the CIRCLE ITEM command.
The WHEEL command has the format:
LINE 9 numbers (or 8 numbers and a colour)
The first three numbers are X,Y,Z of the center of the inner circle.
The second three numbers for a vector orthogonal to the wheel. Make sure
that these first two vectors do not fall on one line with the origin!
The seventh number is the radius of the inner circle. The eigth number is the radius of
the outer circle
There should either be a nineth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of WHEEL commands should be closed with the WHEEL ITEM command.
The PLANE command has the format:
LINE 14 numbers (or 13 numbers and a colour)
The first three numbers are X,Y,Z of the lower-left corner of the plane.
The second three are for lower-right, the next three for upper-right,
and the next three for upper-left. The 13-th number is the line-density in the
plane.
There should either be a 14-th number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of PLANE commands should be closed with the PLANE ITEM command.
The DASH command has the format:
DASH 7 numbers (or 6 numbers and a colour)
The first six numbers are X,Y,Z of the begin and end point of the line.
There should either be a seventh number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of DASH commands should be closed with the DASH ITEM command.
With the RESIDUE command you can tell WHAT IF to display residues. The
residues will be coloured using the present colours in WHAT IF.
The keyword RESIDUE must be placed in the first seven columns of the
line. It must be followed by either a residue, or by a residue range.
This residue input follows the same rules as normal WHAT IF residue
input.
A set RESIDUE commands should be closed with a RESIDUE ITEM command.
The ALLFIL keyword LINATOM should be followed by residue-1/atom-1 and
residue-2/atom-2 and a colour. The two indicated atoms will be
connected by a line of the colour given. Residues can be given
as usual in WHATIF (however, if you use O type residues, put the
O and the residue name together without blank inbetween).
A set LINATOM commands should be closed with a LINATOM ITEM command.
With the CALPHA command you can tell WHAT IF to display an alpha
carbon trace. The apha carbons
will be coloured using the present colours in WHAT IF.
The keyword CALPHA must be placed in the first six columns of the
line. It must be followed by either a residue, or by a residue range.
This residue input follows the same rules as normal WHAT IF residue
input.
A set CALPHA commands should be closed with a CALPHA ITEM command.
The DOT command has the format:
DOT 4 numbers (or 3 numbers and a colour)
The first three numbers are X,Y,Z of the dot.
There should either be a fourth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of DOT commands should be closed with the DOT ITEM command.
The BALL command allows you to draw a sphere of dots around an atom.
This option functions similar as the DOTATM command in the GRAEXT menu.
The keyword BALL must be placed at the first 4 positions of the line.
It must be followed by a residue number and the name of an atom
in that residue. The rest of the ALLFIL file will be mis-interpreted
if you make a mistake in the atom name.
The sphere of dots will get the colour that the atom has in WHAT IF.
A set of BALL commands should be closed with the BALL ITEM command.
The CROSS command has the format:
CROSS 4 numbers (or 3 numbers and a colour)
The first three numbers are X,Y,Z of the center of the cross.
There should either be a fourth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of CROSS commands should be closed with the CROSS ITEM command.
The CONE command has the format:
CONE 8 numbers (or 7 numbers and a colour)
The first three numbers are X,Y,Z of the sharp point of the cone.
The second three numbers are X,Y,Z of the center of the blunt end of the cone.
The seventh number is half of the opening angle of the cone in degrees (or
in other words the angle between the central axis and the side of the cone).
There should either be an eigth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of CONE commands should be closed with the CONE ITEM command.
This will cause WHAT IF to create a MOL-item, and store it in a
MOL-object.
The HAT command puts a dotted spere surface limited by the intersection
of a cone and a spere at the screen. The cone will not be displayed.
The HAT command has the format:
HAT 9 numbers (or 8 numbers and a colour)
The first three numbers are X,Y,Z of the sharp point of a cone, just like
in the CONE command.
The second three numbers are X,Y,Z of the center of the blunt end of a
cone, just like in the CONE command.
The seventh number is half of the opening angle of a cone in degrees (or
in other words the angle between the central axis and the side of the cone).
The eigth number gives the dot density for the dotted surface. Good values
range from 8 to 12. Higher numbers are allowed, but somewhere near 20 WHAT IF
will no longer treat you as a friend.
There should either be an nineth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A set of HAT commands should be closed with the HAT ITEM command.
This will cause WHAT IF to create a MOL-item, and store it in a
MOL-object.
The TRICONE command puts a dotted spere surface limited by a triangle. The
corner points of this triangle are the projection of three vectors X, Y and
Z on a sphere with radius R and center C.
with
The HAT command has the format:
HAT 15 numbers (or 14 numbers and a colour)
The first three numbers are the coordinates of the center C of the sphere. The
next 9 numbers are coordinates of 3 points (X, Y, Z). The planes X,Y,C Y,Z,C and Z,X,C
cut a sphere with radius R and center C along three curved lines. The 'triangle' the
triangle formed by these three lines on the sphere will be filled with dots.
The 13-th number is the radius R of the sphere. The 14-th number is the dot density
for which good values range from 8 to 12. There should either be an 15-th number
that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
A series of TRICONE commands should be closed with a TRICONE ITEM command.
The TEXT command has the format:
TEXT 4 numbers (or 4 numbers and a colour)
The first three numbers are X,Y,Z of the origin of the text label.
There should either be a fourth number that corresponds to the colour
in the usual manner (colour is number from 1 till 360), or one of the
normal colours is written out in full.
The line immediately after the TEXT should hold the actual text to be used
as label.
Instead of TEXT you can also use LABEL.
The MOLLAB command has the format:
MOLLAB 4 numbers
The first three numbers are X,Y,Z of the origin of the text label.
Thefourth number is the MOL-object in which this label should be
stored.
The line immediately after the MOLLAB should hold the actual text
to be used as label.
The CENTER command has the format:
CENTER 3 numbers
The three numbers are X,Y,Z of the new center of the screen
The center command should preferably be used as the first, or the
second to last command in the file (END should be the last one).
The SCALE command has the format:
SCALE 1 numbers
The number will be the new scale factor at the screen.
Reasonable values when working with proteins are 0.1 - 1.0.
The END command has the format:
END
The END command should be the last command in the file.
There are a few more commands in this menu. You can play with those
at a moment that you have realy nothing better to do. They are all bugged
one way or another.
The following options are impossible to intelligently catergorize in
any other chapter... :
The command LOOPSP will cause WHAT IF to prompt you for a range of
database proteins. It will than create a movie of spline drawings
(see the RIBBON option in the grafic menu) for all of these.
Click through this movie with the MOV+ and MOV- buttons, or use
the LOOPER option (see the ANATRA menu) to automatically flip
through them.
The command LOOPCA will cause WHAT IF to prompt you for a range of
database proteins. It will than create a movie of alpha
carbon drawings for all of these.
Click through this movie with the MOV+ and MOV- buttons, or use
the LOOPER option (see the ANATRA menu) to automatically flip
through them.
The command SPLPST does roughly the same as the SPLINE option,
however, a solid filled postscript file is generated. You will
be prompted for black and white or colour plots. After that you
are prompted for ranges till you give zero. Thereafter the COLOUR menu
is automatically activated to allow you to have the ribbon in one
colour, but add side chains in another colour. After typing
END in the colour menu, you come back in the SPLPST option and
are prompted for residues for which the side chains should be added
to the plot. The plotfile generated is called PSTPLT.*** in which
*** normally is 101 (every next plot will be a 1 higher number).
The PSTPST and PSTPSL (see below) options make so many alterations
in the soup that it seems wise to use SAVSOU before this option is
used, and RESSOU afterwards.
The command SPLPSL functions identical to the SPLPST command, the
only difference being that a soft gray background is used, and the the
depth-cueing is inverted. I like this one better than the other one...
The command PLANET will cause WHAT IF to prompt you for a residue
range. Araound this range an ellipsoid will be drawn that fits
the surface of the range `optimally`. The ellipsoid will be
a dotted surface.
PLUTOP prompts you for a residue range. It will draw dots on the surface
of every atom in this range, much the same as the DOTATM option does.
It will however solve the traveling sales manager problem for a walk along
the dots, and connect the dots with lines according to the path found.
The main advantage of this option is that it costs much less lines and dots
than the PLUTO and PLUTOS option, and is thus better suited for small
computers (e.g. PCs).
The command COLTST will draw a colour circle. Use this option if you
think that the colour cables are connected incorrectly, or if you think
something is wrong with your machine.
See page 9 of the tutorial for the correct view.
The ARRFAC parameter provides an overall scaling for arrows.
Good values are around 1.0.
The ARRLIN parameter determines the number of sides on arrows.
Reasonable values are around 10.
The colour of an arrow has to be given as a number between 0 and
360 (0=blue; 60=purple; 120=red; 180=yellow; 240=green; 360=blue).
The ARRLNP parameter determines the length of the arrow point.
Good values are about 1.0.
The ARRLNS parameter determines the length of the arrow base.
Good values are about 2.5.
The ARRTHP parameter determines the thickness of the arrow point.
Good values are about 0.5.
The ARRTHS parameter determines the thickness of the arrow base.
Good values are about 0.5.
The radius parameter determines the radius of atoms when you use the
PLUTO (or PLUTO-like) option. So, the Van der Waals radii are NOT
used in PLUTO or PLUTO-like options. Good values are around 0.5.
The stick option determines the thickness of bonds in PLUTO and
PLUTO-like options. Good values are around 0.1.
The bonds drawn by PLUTO and PLUTO like options consist of a series
of lines, rotated around the central axis. The number of lines used
is determined by the LINES parameter.