This is an option only useful to crystallographers.
Solvent flattening has become an often used and powerfull tool over the
last couple of years. One of the problems is still the creation of the
envelop. Automated procedures are available, but they do not always give
the desired result. The MAPEDT option allows you to visually inspect, and
edit an envelop.
To use this option both the electron density map and the envelop should be
present as a normal input map (in MFF format, see the chapter on maps).
The electron density map and the envelop map should have the same dimensions,
and the same sizes; their headers must be identical. The electron density
map may have any value for every grid point. The envelop map should have
one's for the protein region, an zero's for the solvent.
Both maps can be put up at the screen, and one can edit the envelop by simply
picking (groups of) grid points whose value one wants to change.
The main option of the menu activated with the MAPEDT command is GRAMPP. This
is the actual work horse of the whole option. It will take care that the
electron density will be contoured and put at the PS300 screen. It takes care
that the gridpoints from the envelop will be put at the screen as orange
dots for the protein region, and blue (blue is the colour of water) dots
for the solvent region.
Once program control has been passed to the PS300 screen and data tablet,
you can pick envelop dots which upon picking toggle from protein region to
solvent region or vice versa. If you do not want to toggle, you can switch
to modes where every picked dot gets set to solvent, or to protein region.
The following commands are available besides the extra PS300 screen menu
commands:
The command GETMAP will read an electron density map. Since this command is
fully equivalent to the GETMAP command in the MAP menu, the user is referred
to the chapter on map operations.
When WHAT IF reads a map with any of the GETMAP commands, it does not store
the real values, but a scaled value in the range -115 to 115. A scale factor
is determined, and every time upon user interaction this scale factor is
used to internally convert from reals to bytes or vice versa. The sole reason
for this is that it saves 3 megabytes of real memory usage. The user never
realizes this and normally there would not even be a reason for you to know
all this, if it was not for the fact that envelops are treated different.
Envelops are read, and not scaled to keep the byte values equal to zero
and one. Therefore another routine is needed to read envelop maps, and hence
another option. The command GETENV will read an envelop in exactly the same
way as GETMAP reads maps in general. The only difference is internal to
WHAT IF, and is the skipping of the scaling. The user can treat an envelop
map in all aspects the same as a normal map. The GETENV option also asks
the same further questions, and gives the same results at the terminal
as the GETMAP command.
The command PARMAP in the MAPEDT menu does exactly the same as the command
PARMAP in the map menu. Therefore the user is referred to the chapter on
map operations.
The command DEFMAP in the MAPEDT menu does exactly the same as the command
DEFMAP in the map menu. Therefore the user is referred to the chapter on
map operations.
The command SHOMAP in the MAPEDT menu does exactly the same as the command
SHOMAP in the map menu. Therefore the user is referred to the chapter on
map operations.
The default mode of operation for picking gridpoints at the screen is toggeling.
If you do not want to toggle every reflection that you pick but want to set
it to 0 regardless whether it was zero or one before, you can use the FIX0
command.
The command FIX1 makes that every gridpoint picked will be set to one,
regardless is previous value.
The command NOFIX can be used to switch back to toggle mode.
The command GRAMPP will cause WHAT IF to prompt you for the number of the
density map, and the number of the envelop map. If you forgot the numbers,
just type zero to bail out, and use the SHOMAP command to see which maps
are what. WHAT IF will automatically start contouring the electron density
map and after a while prompt you for the number of the mol-object, and
the name of the mol-item in which to store the contours. Thereafter the
requested gridpoints (just like the contour parameters set with the PARMAP
command prior to using this option!) will be send to the PS300. You will
then see that the PS300 screen menu has changed, and that command has been
paased to the PS300 screen menu and the datatablet. Several options are
presently not active, but there are also some new options at the bottom of
the menu. The screen menu options will shortly be described.
The old option (above the line under CHAT) that are still there all react
the same as normally is the case when you type GO in any of the graphics
menus. The only difference is CONT which now centers the screen at a
gridpoint instead of an atom.
YES will make all changes made sofar permanent. NO will undo all changes since
the last time you picked YES. WAIT will do the same as NO, but will also
end the GRAMPP option. CHAT is rather dangerous to use, because it brings
you in the menu which is meant for normal WHAT IF usage (you know, when you
work with molecules and atoms and such). Since there most likely are no atoms
presently available there are several places where the program can crash. An
experienced user however might need this possibility.
Below the line you will see several new menu items. These are:
RFSH, SQUA, CIRC, SPHE, NEXT, FIX0, FIX1, NOFX.
Every time you pick a gridpoint this gridpoint will be marked with a little
purple cross. If you want to remove these crosses, and get all the gridpoints
in the right coloir at the screen (orange for protein region and blue for
solvent region) then you can pick RFSH.
If you only use one plate of gridpoints at a time (you do so by setting one
of the three mapwid parameters to 0 when in PARMAP) you can switch to the next
plate by picking NEXT. This command works in all three directions. It always
takes the plate one gridpoint further away from the origin of the envelop map.
When the edge of the envelop map is reached, this command no longer takes the
next plate, but simply the same plate again.
This command does the same as the MAPEDT menu command FIX0. See above.
This command does the same as the MAPEDT menu command FIX1. See above.
This command does the same as the MAPEDT menu command NOFIX. See above.
The command SPHE takes care that every next pick of a gridpoint will not
only effect that gridpoint, but also all gridpoint within a sphere of 4
Angstroms around this gridpoint. That means that if you are in toggle mode
all point in this sphere will be toggled; and if you have either FIX0 or
FIX1 active, all points within this sphere will be set to 0 or 1.
The command CIRC takes care that every next pick of a gridpoint will not
only effect that gridpoint, but also all gridpoint within a circel with 4
Angstroms radius around this gridpoint. That means that
if you are in toggle mode
all points within this circel will be toggled; and if you have either FIX0 or
FIX1 active, all points within this circel will be set to 0 or 1.
The command RECT will prompt you to pick two gridpoints. These gridpoints
become the corners of a rectangle. All points within this rectangel will now
be effected.
That means that if you are in toggle mode
all point within this rectangle will be toggled; and if you have either FIX0 or
FIX1 active, all points within this rectangle will be set to 0 or 1.