Moloc: Molecular Modelling on UNIX Workstations: 15 Handling Maps [map]
Handling Maps [map]
This utility allows to handle various maps, such as
electron density or Ramachandran-type energy maps.
v: visibility
Contours are divided into bricks, the size of which is
automatically set when generating the contour. This is
done for the sake of gaining display speed. The visi
bility setting determines the criterion according to
which the program decides which bricks are to be dis
played. Contours can be made visible in four different
modi: brick-wise by user definition (p), automatic-
ranged (a), user-range wise (r), translated (t). The
translation option (t) is auto-ranged and extends the
visibility to regions in space which are displaced by a
lattice vector from regions in which a map is given.
However, every brick of the actual map is only dis
played once, and equivalent bricks are drawn on top of
each other.
b: make bricks visible by picking atoms
By picking atoms the contour brick around that atom is
set to visible. All and only the contours, the visibil
ity of which is set to (p), are affected. By choosing a
non-zero pick range, the bricks in the corresponding
neighborhood of the picked atom are lit. In order to
select bricks with the 3d pointer use options p and e.
r: set user range
Bricks in the environment of the center of the display
volume are visible if the center is not farther of the
brick then the specified range. This range applies if
the r-visibility mode is chosen. Automatic ranging sets
the range such as to fill most of the display volume.
g: get map
Several file formats can be read. The user can provide a
list of map files (one per line, and of the specified
format) in a file (e.g. mymaps). When asked for the file
name, the answer @mymaps causes the program to read in
all specified maps automatically. Furthermore, for each
map several contours can be specified by contour level
and color: the line 'map1.mpu 1.3 red 2.5 blue\q on the
file mymaps will cause the program to read in map1 in
.mpu format and to generate a red and a blue contour at
the levels 1.3 and 2.5 respectively. For CONTUR format
ted maps (.ctr) the program expects to find in the same
directory a file called CELL in which the cell parame
ters are given. Such a file is written by the program
FSFTOCTR which customizes maps generated by the PHASES
program. PHASES maps (.fsf) are periodically extended
to cover the whole unit cell surface. Together with the
translation option for visibility, automatic coverage
of all space is provided.
k: contour map
The program asks for a level at which a contour should
be calculated. If a map is only two-dimensional, sev
eral contours are calculated: the first at the speci
fied level (say d over the minimum) all further
contours have than a mutual spacing of d. The represen
tation is still three-dimensional with the third dimen
sion indicating the contour level.
c: color contour
A selector with the available contours is shown. The
chosen one can be recolored.
n: transfer contour into entry
A contour can be copies into an entry to enhance the
palette of display possibilities (mostly for documenta
tion). There are two options: to transfer the contour
as a whole or to transfer just the bricks marked visible
(see picking mode under the visibility option). The
latter can reduce the size of the resulting entry con
siderably!
d: delete contours
t: delete maps
A selector with the available contours (maps) is shown.
Several can be chosen. The ones to be deleted become
marked with a 'd\q. Upon leaving the selector they are
removed.
f: draw frame of a map
A frame is drawn showing the extent of the map. It is
two or three-dimensional in accord with the map dimen
sion. Graphically, the frame is handled like a contour.
s: select map for examination
For examination of maps the user has to choose here
which map to examine. When no map is chosen, option e
changes its function to lighting contour bricks (see
help of p and e).
e: examine map
Map values for points inside its frame can be examined.
For that purpose the 3-d pointer is moved to the desired
position. This is done by pressing down the shift key
and moving the mouse with the middle button pressed (x-
y motion); also pressing the left key moves in z direc
tion. The value of the map at the 3-d cursor position is
extracted by issuing a left-button click while the con
trol key is pressed. If no map is selected for examina
tion, this operation lights bricks containing the 3d-
pointer for all visible contours which are in the pick
ing mode of visibility. This is quite analogous to the b
option except that the 3d-pointer determines which
bricks are lit instead of the picked atom. In this case
a middle mouse-button click unlights the corresponding
bricks.
p: 3d-pointer on <-> off
The p3d-pointer is removed or inserted at the center of
the visible volume.
o: reset orthogonalization
With the map goes a orthogonalization which is charac
terized by three letters indicating the axes. If capi
tal letters are used, the first letter tells that the
corresponding axes (of unit cell- and orthogonal sys
tem) are aligned, the axes of the second letter lie in a
common plane together with the first axes. The Xplor
convention is XYZ, i.e. X and x-axes are identical, XY
and xy-planes are identical too. For lower case let
ters, the Brookhaven convention applies.
m: select transformation (to move contour)
If a contour of a map is needed, which corresponds to a
transformed position (e.g. crystallographically symmet
rical) a transformation can be specified here. It will
be taken from the set of available transformations, to
which stored ones can be read in from a file.
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