The ideas behind hydrophobic moment calculations are described well
by David Eisenberg in a series of articles about 15 years ago.
In WHAT IF that idea got generalised. Rather than calculating
hydrophobic moments, we calculate all kinds of moments. After all,
a hydrophobic moment is nothing but a Fourier transform over the
properties of residues (in a small window). Originally the property
was supposed to be hydrophobicity, but in WHAT IF every property
that you can get in a table can be used.
The basic ideas behind this menu is that you first read some of the
Eisenberg articles. Thereafter you figure out how TABLES work in
WHAT IF. Thereafter, you look in the file PROPS.VAL (in the
dbdata directory) an see what properties we have already entered
for you. If needed you enter your private favourite property to
this file.
After doing all that, you are ready for the calculations.
Be aware that these calculations use the sequence as
is present in the SOUP.
The command SETPRP will prompt you for a table number, table title
and sequence range, just like most TABLES menu options would.
It will fill the table with the property values corresponding to
the residue in the SOUP and the selected property (see the PROPTY
parameter for property selection).
The option CLCMOM will first prompt you for an input table. This
should be the table with property values that you made with the
SETPRP command, or any other table that you wish. Thereafter it
will prompt you for a table number, table title
and sequence range, just like most TABLES menu options would.
The property moment will be calculated using the window size
and repeat angle as set with the WINDOW and ANGLEM parameters.
I forgot what I wanted to achieve with this option. It does something,
but reverse engineering seems required to figure out what....
The command SHOPAR will show you the (three) parameters that are
relevant for the HYDRO menu.
You can set the following parameters:
Width of the window over which the moment calculation runs
Property type number as indicated in the file PROPS.VAL. This is
the property number that SETPRP asks you to give.
Repeat angle for moment calculation. Use 100 for helix and 180
for strand.