WHAT IF allows you to use the graphics window
as a simple two dimensional graphics
device.
The general option GRATWO brings you in the menu from which the two dimensional
graphics options can be executed. All two dimesional graphics
options like phi-psi plots, or B-factor plots etc. are made
pickable. This means that you can pick the items to label them,
or to see the underlying structure.
In all plots (eg phi-psi, or B-factor plots) the colour
will be the one as set for the alpha carbon.
Except in the case of
phi-psi plots
which are screen filling,
all plots take only part of the screen. You will be
prompted for the position of the plot at the screen.
WARNING. Two dimesional graphical MOL-items are normal three dimensional
items that often have all Z-coordinates equal to zero. Therefore if you rotate them
90 degrees you see nothing any more!
The following options are available:
The command PHIPSI prompts you for residue ranges and will generate
a Ramachandran plot which will be stored in a MOL-item. Look also
at the more general and more interactive options RAMAON and RAMAOF.
In the Ramachandran plots you see contourlines. These lines represent
a 10, 20, 30, 40, 50 percent chance that a residue falls outside
those lines (these percentages are calculated from the proteins
that were selected to sit in the WHAT IF SCAN3D database).
The colour code is like for the DSSP menu: blue is helix, red=strand,
green=turn and loop. Diagonal crosses are 'normal' residues;
orthogonal crosses are glycines and ope squares are prolines.
This command will prompt you for molecule numbers just like
the PHIPSI command does. It will however, also ask for a residue
type.
All residues of the requested type that belong to the requested
molecule(s) will be labeled in the Ramachandran plot.
The command RAMAON creates the interactive Ramachandran plot.
to the alpha carbon colour (default=green). The phi-psi plot can be looked at
in stereo. The third dimension in this plot indicates the deviation of perfect
(being 0 or 180 degrees) omega angles.
The interactive Ramchandran plot is connected to the soup and to the
sequence bar at the bottom of the screen. That means that if you change
the colour of the alpha carbons of the residues represented in the
interactive Ramachandran plot, the crosses in the plot will change
colour too. Also it does not matter where you pick, an atom, the
sequence bar at the bottom of the screen, or the interactive
Ramachandran plot, all three of them will be lebeled.
The button RAMACH in the menu at the bottom of the screen will
toggle the visibility of the interactive Ramachandran plot On/Off.
The command RAMAOF switches off the interactive Ramachandran plot that
you generated with the RAMAON option.
The button RAMACH in the menu at the bottom of the screen will
toggle the visibility of the interactive Ramachandran plot On/Off.
In many cases WHAT IF creates data per residue and displays this, or writes
it out in a file. In most of these cases these values (whatever they are, quality,
average shift, torsion angle, etc.) are also stored as the so-called property values.
These property values can be plotted with this option. Property values are
shown in brackets (as Prp=value) on the first line of the output per residue
if you issue the LISTA command.
This option makes a plot of the average B-factor per residue versus the
residue number. This option will of course, only work for molecules that have
atomic B-factors, and not for models or NMR structures.
This option makes a plot of the GROMOS energy content per atom summed over
the whole residue versus the residue number. You will be prompted for the
energy term to be used. This option has some help in it. Of course, this option
only works if you have calculated the energy per atom first (See GETETM
in the GROMOS menu) for which you will need GROMOS installed on your machine.
The command PPPSRI will cause WHAT IF to generate a phi-psi plot according
to Shrinivasans method. Just try it, it does not take much time. (Phi are
the bars above the central bar, Psi is below it).
The command ATMLAB will cause WHAT IF to ask you to give a residue
number and an atom name (in that residue). After
that you will be promted for a text line (of maximally 80 characters).
This textline will be placed next to the requested atom. The size of the
charaters can be selected. I suggest you use the defaults. The text is not
screen oriented. That means that if you rotate the molecule, the text
will also rotate. You should therefore place the labels only when the final
orientation for the photo or slide has been chosen. Atom labels are normal
mol-items. They can therefore be rotated translated, but also plotted.
This option is 100% identical to the LABATM option in the LABEL menu.
Ramachandran plots, B-factor plots, etc., are all pickable. If, however,
you have a whole screen full of information, you might want to
get rid of this pickability because you might accidentally pick
these plots (or their remains) at moments that you dont want that.
NOPIC2 will irreversibly make the two-dimensional plot unpickable.
Several options in the bar of pickable options at the right side of the screen
have a slightly different function when used with two dimensional
objects than when used with three dimensional objects (such
as molecules). The most prominent differences aoocur in NEIM and CONT.
NEIM will also allow you to pick in a two dimensional graphics object.
Pick there where you intuitively expect the pick, except with contact
boxes where the lower left corner needs to be picked.
WHAT IF will show the local environment
of the residue(s) that correspond with the picked box, cross, etc.
This environment is not pickable.
Pick INIT to remove this local structure.
The residues will be translated from their normal soup positions to such
a position that they roughly are 'near' the cross, contact square, etc.
This way you
do not have to search through the whole graphics screen.
CONT will ask you to pick something. This atom, box, cross, etc.
will now become the center of the graphics.
The same parameters that are active in the ANACON menu (see chapter on contac
analysis) can be used from the two dimensional graphics menu. Some of them
however are rather useless here.
There are about ten parameters that can be changed to influence what the pictures
at te screen will look like, only two of those are useful for
the GRATWO menu.
The user changes these parameters by name. They are called:
FRMCOL = Colour of frame around plot (only plots that have a frame...)
NEICOL = Colour of neighbouring residues after picking
The other parameters are explained in the ANACON menu, under PARAMS.