Do not expect all kinds of fancy NMR options, we just implemented
some options that other programs don't have and that were easy to
make within the WHAT IF working environment.
Several options in this menu will display protons. If you do not have protons
in the soup, but their positions can unambiguously be calculated, the
protons will be displayed (but will in that case not be pickable).
The command GETDIA can be used to read a DIANA output file. You will be
prompted for the file name and for the set name.
One of the problems with solving structures by NMR is that there are always
very many (hopefully very related) structures that fulfill the NOE requirements
to the same extend.
One therefore has to operate on many molecules at the same time. WHAT IF
is especially good in doing so because of the very large number of
molecules/residues it can hold in memory.
All multi molecule options expect a list of molecules to work on. The first
molecule in this list is the main molecule (for example the one on
which to superpose all other ones). The USEMLS option can be used to
define the list of molecules.
The command USEMLS has to be used before any of the other multi-molecule
options. With USEMLS you define the list of molecules to be used in
subsequent multi-molecule options. Use USEMLS again if you want to
change the list of molecules to be used.
The first molecule in the list is the main molecule. Superpositions will be
done on this molecule. Comparisons will be made with this molecule. When
you are prompted for a residue range, you should only give residues in this
molecule, WHAT IF will then automatically determine the equivalent residues
in the other molecules.
The list of molecules should at least hold two molecules.
All molecules in the list of molecules should be covalently identical. That
means that they should have the same sequence, the same atoms, but are
allowed to have completely different structures.
The option LSTMLS will tell you which molecules were activated the
last time you used USEMLS.
The command CHKMLS will cause WHAT IF to move over the list of molecules,
and check if they are all covalently identical. If they are not, you can still
try to run the multi-molecule options, but a crash might be your reward
for that...
This option will prompt you for a file with file names. This file
should hold one filename per line. Those dfiles should be PDB files
WHAT IF will execute the GETMOL command for each file in this
file name list. Include the full directory path as part of the
file names.
Be careful there are limits to the numbers molecules, residues and
atoms WHAT IF can have in its SOUP (500, 4000 and 32000 respectively;
status June 1997).
The option SUPMLS will first show you a small mini menu. From this menu
you can decide to either automatically superpose all molecules on the first
one, or define ranges yourself to use for superpositioning.
The automatic
superposition will simply superpose the second molecule on the first,
the third on the first, etc. All matrices will automatically be
applied. So in contrast to superpositions in the SUPPOS menu,
you do NOT have to use the APPLY option at the end.
In case you choose to manually define the residues on which to superpose,
you will be prompted for these residues. Here you can give
residues in the first molecule of the molecule list defined with the
USEMLS option. In all other molecules the equivalent residues will be
selected to determine the superposition transformation. The resulting
superposition transformation per molecule will be applied to that whole
molecule.
The option MOTMLS will run the MOTIVS option (see chapter on SUPPOS)
on the
first molecule and the second, the first and the third, etc. All matrices
will automatically be applied. So in contrast to MOTIVS in the SUPPOS menu,
you do NOT have to use the APPLY option at the end.
It is rather likely that the residues used to superpose on are not the
same for all molecules.
The option CAMLS will cause WHAT IF to prompt you for a set
of residues in the first molecule that you gave with the
USEMLS option. It will than display the alpha carbon traces
of all equivalent residues in all activated molecules.
The molecules will be colored purple till yellow in the
order you typed them in the USEMLS option. The first
C-alpha trace will be drawn in green
The option ZONMLS will cause WHAT IF to prompt you for a set
of residues in the first molecule that you gave with the
USEMLS option. It will than display all atoms
of all equivalent residues in all activated molecules.
The zones will be colored purple till yellow in the
order you typed them in the USEMLS option. The first
zone will be colored by atom type.
The option AVRMOL assumes that all molecules in the soup are proteins that
are chemically identical, but have different structures. The option will
cause WHAT IF to generate one more molecule in which every atom is
placed at the center of gravity of all equivalent atoms in soup. This
averaged molecule has of course not proper geometry!
The command TOPOLO will prompt you for the name of a (new) topology file. This
file will than be read and WHAT IF's entire internal administration will be
updated. Be aware that the soup will be initialized by this command. Also,
many files saved with commands like SAVSOU in the SOUP menu can now no longer
be read....
The command BBBALL will prompt you for a residue range. It will than draw the
backbone for this range as a normal stick model, but with the hydrogens
included if requested.
On top of that, small dotted spheres will be added for all atoms.
The command GRABBD will prompt you for a residue range. It will than draw
the N, C-alpha and C in the
backbone for this range as a normal stick model, but with the nitrogen
hydrogens included.
On top of that, small dotted spheres will be added for all atoms shown.
The option PEPLAN will prompt you for a range of residues. It will show
for all residues in this range 2 (1 for proline) little triangles
made up respectively of the backbone atoms N, C, O and C, N, N-H.
This option will cause WHAT IF to prompt you for a distance cutoff. It will
then consider all groups of alpha carbons that fall within this distance
of each other, and determine the hand of the two residues that make a contact
and send a cross to the graphics screen colored as function of these
two hands.
This option does exactly the same as the BPLANE option in the GRAEXT
menu.