By default all atoms are blue, unless you give them a colour. Several
WHAT IF options give other colours automatically. This then is either
one colour for all atoms, or default colours.
If you use default atom colours (option COLATM)
all nitrogens will be blue, oxygens red, carbons green,
phosphors purple, and sulphers dirty yellow. See appendix B for
the possible colours you can use.
In WHAT IF every atom has many parameters permanently
attached to it, these parameters stay attached to the atom untill they are
overwritten. One of these atomic parameters is the colour. The above mentioned
default colours will be used for every atom send to the screen. The menu COLOUR
allows you to change the colours of atoms
(or whole residues).
If you use the command DIRECT in the GRAFIC menu, or click the DIRECT
button in the row of boxes at the bottom of the screen, the so called
direct mode is activated. In direct mode all graphics actions are
directly shown at the screen, without the use of MOL-items or
MOL-objects. (Toggle all MOL-objects off if nothing happens).
Protons will always get a colour that differs a very little bit
from the colour of the heavy atom they are connected to.
This is the default colouring scheme. The command COLATM causes WHAT IF to
prompt you for the residue range. The residues you give will get the following
atomic colouring scheme: all nitrogens become blue, oxygens become red,
carbons become green, and sulphers become dirty yellow. Residues outside the
requested range keep the old colouring scheme.
The command COLABF does the same as the command COLBFT, with as only difference
that The average atomic B-factor is calculated first, and this value is
used for all atoms in the residue. The atomic B-factors that are attached
to the atoms will not be averaged, so the soup remains unchanged,
only the avaerage value will be used.
All averaged B-factors are then
divided into 12 bins, and coloured in 12 steps from cold to hot, blue to red.
The divisions are made such that the colour-value is a linear function of the
B-factor. WHAT IF will prompt you for the residue range. Only the residues you
give will be used in the calculation of bins etc. and get their colours
changed. You can change the range between which the colours are ranged
with the COLRNG command, be aware however that WHAT IF always makes bins
that are ten HUE-value steps wide, so if you colour for example from
yellow (HUE=180) to green (HUE=240) you will only get 6 colours.
The command COLACC causes WHAT IF to
prompt you for the residue range. The residues you give will get coloured
atom by atom blue till red as function of their accessibility. See
also COLRNG and COLBIN.
The command COLBFT changes the atom colours such that the coldest
atom (that is the one with the lowest crystallographic B-factor) becomes
blue, and the hottest (highest B-factor) becomes red.
All B-factors are then
divided into 12 bins, and coloured in 12 steps from cold to hot, blue to red.
The divisions are made such that the colour-value is a linear function of the
B-factor. WHAT IF will prompt you for the residue range. Only the residues you
give will be used in the calculation of bins etc. and get their colours
changed. You can change the range between which the colours are ranged
with the COLRNG command, be aware however that WHAT IF always makes bins
that are ten HUE-value steps wide, so if you colour for example from
yellow (HUE=180) to green (HUE=240) you will only get 6 colours.
The command COLCHG changes the default atom colours such that the most negative
atom becomes
blue, and the most positive one becomes red. All charges are
divided into 12 bins, and coloured in 12 steps from negative to positive,
blue to red.
The divisions are made such that the colour-value is a linear function of the
charge. WHAT IF will prompt you for the residue range. Only the residues you
give will be used in the calculation of bins etc. and get their colours
changed.
After you have analyzed a GROMOS output (see the GETETM command
in the chapter on
GROMOS) you get a table
of individual atomic energy values. GETETM (See the chapter on energy
calculations and GROMOS) causes WHAT IF to prompt you for
the name of the file with these energy values. If you ran the analysis from
within WHAT IF, then it uses the file created in that process as the default.
WHAT IF will then read this file. COLETM uses the same colouring algorithm as
COLBFT does. The only difference is that COLBFT uses the B-factor range
from cold to hot to go from blue to red; COLETM uses the energy range from
low to high to colour from blue to red.
You can change the range between which the colours are ranged
with the COLRNG command, be aware however that WHAT IF always makes bins
that are ten HUE-value steps wide, so if you colour for example from
yellow (HUE=180) to green (HUE=240) you will only get 6 colours.
The command COLHSP will cause WHAT IF to prompt you for the name of an HSSP file
(see the chapter on HSSP). You will also be prompted for the number of the molecule
in the soup that should correspond with the HSSP file. In principle the HSSP file
should be based on this molecule in the soup. However, to allow you to fool
WHAT IF, you will be asked if the molecule in the soup and the HSSP file
should match exactly. If you say YES, error messages are issued upon detection
of differences in the sequence in the soup and the HSSP file. If you say NO,
different sequences in the soup and the HSSP file are allowed. This is nice if you
want to use the HSSP file of a wild type molecule to colour a mutated molecule.
There is no way to predict what will happen if the HSSP file and the molecule in
the soup in no way belong together.
COLHST (=Colour Helix, Sheet and Turn) will colour the residues
according to their secondary structure as
determined by DSSP. (If the secondary structure has not been determined
yet, then this will be done first automatically by WHAT IF). the following
colour scheme is used:
H (helix) : 30 BLUE-ISH PURPLE
3 (3-10 helix) : 50 PURPLE
S (sheet) : 130 RED
T (turn) : 290 BLUE-ISH GREEN
C (coil) : 260 GREEN
(coil) : 260 GREEN
The command COLSMC will prompt you for a residue range and a colour.
All residues in this range that make a crystal contact in the crystal will
get the indicated colour. You will also be prompted for an environment.
Here you should give the molecules that belong together in one dataset or
PDB file.
This option is rather useless for models and structures solved by NMR.
The command COLREF will prompt you for residue range(s).
For all residues in this range the Z score for geometric errors will
be calculated. Atoms with perfect geometry (only bond lengths and bond angles
with covalently connected neighbour atoms are evaluated)
get coloured green (for perfect) to red (for 10 sigma or more deviating
from perfect).
COLTYP allows you to set all atoms of all residues, of one or more types
to the same colour. You will first be prompted for the residue range and
for the residue types. Then you will be prompted for the colour.
The colour should be a HUE-value between 1 and 360. If you do not know what
HUE-values are, just hit return, and some info will pop up.
All requested residues
within the given range will get the given colour.
COLZNS allows you to set all atoms of multiple zones of residues
to the same colour. You will be prompted for that colour and
for the residue ranges.
All atoms in all residues
within the given ranges will get the given overall colour.
The command COLBB will cause WHAT IF to prompt you for a residue range and
for a colour. All backbone atoms (N, C-alpha, C and O) of this range will
get the requested colour. This option only works on proteins.
The command COLMOL will cause WHAT IF to prompt you for a colour and for a
molecule number. This whole molecule will get the requested colour. This
option can be used for all types of molecules (protein, nucleic acid,
drug, group of waters).
COLCLU will prompt you for a cluster and a colour. All atoms in all residues
in that cluster will get the requested colour.You need to run the
SETCLU option in the CLUFAM menu before you can use this option.
COLFAM will prompt you for a family and a colour. All atoms in all residues
in that family will get the requested colour. You need to run the
SETFAM option in the CLUFAM menu before you can use this option.
The command COLH2O will cause WHAT IF to prompt you for a colour. It will
then colour all waters in the soup accordingly (if there are any of course).
The command COLSCH will cause WHAT IF to prompt you for a residue range and
for a colour. All side chain atoms of this range will
get the requested colour. This option only works on proteins.
The command COLSPC will show several special pre-defined colouring schemes.
You can just loop through them and say YES when you see a scheme that you like.
I suggest you just take a look what is in there.
The command COLBIN will prompt you for a residue range. All colours will
be scaled such that all colours occurr roughly equally often. For example,
if you have your molecule coloured as function of the B-factor from
blue till red, and one residue has a B-factor much higher than all others,
then you will see a virtually completely blue molecule with one red residue.
COLBIN will cause the 8% atoms with the highest B-factor to all get the same
colour (red in this example); the next 8% atoms with highest B-factors
will get a little bit blueish red, etc. The 8% residues with the lowes
B-factors will get dark blue. If you choose another colour range you can
get another percentage of atoms per colour bin. Just experiment a bit.
Several options in WHAT IF add values to residues (e.g. hydrophobic moment
calculation, HSSP mutability, etc.). The property value of each residue
is shown as (Prp=value) on the top line of the LISTA output of each
residue.
COLPRP colours all residues according to their property value.
The property value per residue is used for all atoms in the residue.
All property values are
divided into 12 bins, and coloured in 12 steps from low to high, blue to red.
The divisions are made such that the colour-value is a linear function of the
property value. WHAT IF will prompt you for the residue
range. Only the residues you
give will be used in the calculation of bins etc. and get their colours
changed. You can change the range between which the colours are ranged
with the COLRNG command, be aware however that WHAT IF only uses bins
that are ten HUE-value steps wide, so if you colour for example from
yellow (HUE=180) to green (HUE=240) you will only get 6 colours.
Several colouring options map a physical parameter range on a colour
range. Eg. COLBFT colours from blue till red as function of the B-factor.
If you want to change the colour extremes of those ranges, you can use
the COLRNG option. WHAT IF will prompt you for the two extremes. You are
not allowed to give twice the same colour. Everything else is possible,
also inverting the ranges (go from red till blue rather then from blue
till red). WHAT IF will not always do what you expected if you use 360
as one of the extreme colours.
The command COLSHF is a dirty hack that allows you to shift
all colours in a certain range. You are prompted for the lower
and higher colour extreme of a colour range. All atomic colours
within this range are shifted upwards so that no atoms are left
with a colour within this range. So if the range is 40 wide, all colours
within this range will become 40 bigger.
The command COLREP will cause WHAT IF to prompt you for an old
and a new colour. All atoms that have the old colour will get
the new colour. This is in the soup, and only in DIRECT mode also
in the graphics window. This option only operates on heavy atoms.
If you have protons in the soup, their colour will be updated
automatically.
COLROW colours according to the true false values in an atomic corelation row.
See the SEARCH menu description for the generation of these rows. Every atom
for which the atomic parameter row value is true will become green. If the
value is false, the atom becomes red. You need to create a row before you
can use this option of course.
The command COLTAB colours the atoms as function of the values in a table.
You will be prompted for the table number and for the residue range. The
residues in this range will be coloured as function of the corresponding
table value.
The residue with the lowest becomes
blue, and the the one with the highest table value becomes red.
You can change the range between which the colours are ranged
with the COLRNG command, be aware however that WHAT IF always makes bins
that are ten HUE-value steps wide, so if you colour for example from
yellow (HUE=180) to green (HUE=240) you will only get 6 colours.
You need to create at least one table before you can use this option
of course.
Several hidden options can be found in the colour menu. These are often
quick fixes written on request. It therefore seems unlikely that these options
will be fully documented. There is also no guarantee that they will all work.
Just try them out. Perhaps you will find something useful among them.
Type HIDDEN to get a list of the hidden options.