Reading data
readins insfile
readhkl hklfile
pg set point group
Filter
filter start filter routine
angdistmax set angular distribution
intmin set minimal intensity
nhklmin set minimal redundancy
thetamin set minimal theta
Build/Modify crystal description
addface add face (x y z d)
addfacehkl add face (h k l d)
addfaceperp face1 face2 dist
addfacesum face numbers
buildcube a simple cube
buildsphere select one of 7 dodecahedron models
bestsphere search best dodecahedron
deleteface delete faces
face set face parameters
replaceface replace faces
Options
angmin minimum angle between rotaxes
angmax set maximum tilt angle
centric centric shape on/off
correction ABST/ABSG
extreme set initial refinement shift
highindex set high index
improve set refinement improvement threshold
initdistance set initial distance
phi set phi start, stop and delta
tol set refinement tolerance
weight set weights for R2 calculation
Refinement commands
amoeba amoeba distance
crystrot crystal rotations
crystrot1 single rotation
crystrotface single rotation
crystrothkl single rotation
crystrotsimplex simplex crystal rotations
distance refine face distances
tilt refine face tilt
volume refine volume
Graphics
colour axes/bg/circle/cosi/coso/faces/fg
croty continuous rotation
mode cone/stereographic/ajmd/z
onerot rotate picture
partialrot rotate picture
plotaxes do/donot plot crystal axes
plotcorner do/donot plot corners
plotlab do/donot plot cartesian axes
pointsize point size in pixels
posx window position
posy window position
size window size
vertical put view direction vertical
viewdir view along hkl direction
viewpartial set rotation angle for partialrot
viewperp view perpendicular to face
viewrot rotate view vector
viewspeed rotation speed
viewxyz view along cartesian vector
Misc
copy create new ins file
edit edit ins file
exit end program
hkl single reflection information
plot use platon to display shape
reduce reduce face indices
status program status
test consistency test
workfile set workfile name (subfile)
writehkl write (filtered) hkl file
You may also visit the explanation of
internal commands: aliases, flowcontrol etc.
Reading data
The command readins
filename reads name.ins
in PLATON format. For running EUHEDRAL, name.ins
must at least contain a CELL line and the absorption coefficient,
given by an ABST or ABSG line. If a crystal description is available, it should
be given with the corresponding FACE cards. If no crystal description is
available, it can be generated with the EUHEDRAL commands
buildcube,
buildsphere,
or bestsphere.
If you provide an orientation matrix name.rmat
it will be used (see coordinate systems).
It is necessary to run readins
at every program start of EUHEDRAL.
The command readhkl
filename reads name.hkl
in SHELXL-HKLF4 format.
The reflection file must contain the direction cosines, as described in the
SHELX76 manual. Please be aware that the reflection indices and direction
cosines must correspond to the CELL line of the ins file. If this is not the
case, you can use PLATON for a transformation of the reflection file,
before you use EUHEDRAL.
Note: EUHEDRAL only uses the default settings of 32 point groups,
see pg.
Reflections with intensities lower than 3.0*sigma are ignored by
readhkl (so negative intensitities are also
ignored).
Once the EUHEDRAL command filter had been used and the subfile.hkl is present,
it is not necessary to run readhkl at every program start.
With the command pg
pointgroup the point group symmetry is set. This information is used
for the determination of the redundancy in the
filter routine, and for the
calculation of R values.
Only the 32 standard settings of the point groups are known to EUHEDRAL. (Note:
You can always apply a transformation matrix to the reflection indices and the
corresponding direction cosines by using the program PLATON before.
Example: reflections in the non-standard point group 2mm must be
transformed with PLATON into the standard point group mm2).
The available point groups are:
1 -1
2 m 2/m
222 mm2 mmm
4 -4 4/m 422 4mm -42m -4m2 4/mmm
3 -3 312 321 31m 3m1 -31m -3m1
6 -6 6/m 622 6mm -6m2 -62m 6/mmm
R3 R-3 R32 R3m R-3m
23 m3 432 -43m m3m
Filter
The command filter is used to generate a
subset of the original reflection
file. This subset can then be used for the refinements with EUHEDRAL. With the
graphical display you can check the distribution of the reflections (incoming
and outgoing beam) in reciprocal space. Filter options
Build/Modify crystal description
Syntax: addface
x y z distance
Add a new face to name.ins, perpendicular to a
cartesian xyz direction
(see coordinate systems).
Interesting xyz directions can be found using the command
test.
Syntax: addfacehkl
h k l distance
Add a new face to name.ins by supplying hkl indices.
Syntax: addfaceperp
i j distance
Add a new face to name.ins,
perpendicular to two existing
faces i and j.
Syntax: addfacesum i j ....
Add a new face to name.ins as a sum of already existing faces.
Enter a list of faces (at least 2).
The facenormals of the contributing faces are summed. The distance
is the average of the contributing faces. See also
replaceface.
Syntax: buildcube distance
The command buildcube generates a simple
cube, which can then be refined
with crystrot and the other EUHEDRAL commands. An
initdistance value for the
crystal faces (crystal size) must be supplied.
Buildcube will overwrite
the FACE cards of the current ins file.
Syntax: buildsphere
distance type
The command buildsphere generates a simple
dodecahedron, which can then be
refined with crystrot and the other EUHEDRAL commands.
An initdistance value
for the crystal faces (crystal size) must be supplied. One of seven different
dodecahedrons (rhombohedral and pentagonal) can be chosen.
Buildsphere will overwrite the FACE cards
of the current ins file.
Syntax: bestsphere
tolerance distance refinementtype
The command bestsphere refines seven
different (rhombohedral and pentagonal)
dodecahedrons by volume or distance refinements in order to find a suitable
starting model for the EUHEDRAL refinements. All refined models are stored in
the files model1.ins to model7.ins, so that they can be read later.
refinementtype is a string build of the
characters
v,
a and
d (for
volume,
amoeba and
distance). For example
refinementtype vd will first perform
a volume refinement followed by a distance refinement.
The best model overwrites the current ins file.
To speed up this time consuming command, it may be advisable to set the
tolerance to a value of 0.1, using the EUHEDRAL command
tol.
Syntax: deleteface i ....
Enter a list of faces (at least 1).
These faces will be removed from name.ins
(if the resulting model
remains valid). Please note that the labelling of the faces
may change after deleting one or several faces.
Syntax: face n h k l d
You can change the face indices h k l and/or
distance d of a single face
n which is already defined in
name.ins.
See also edit to edit name.ins.
Syntax: replaceface i j ....
replace faces
Enter a list of faces (at least 2). The sum of these faces will
be added to the *ins file, and the contributing faces will
be removed from the *ins file.
Please note that the labelling of the faces
will change after replacing several faces.
Options
Syntax: angmin angle
See crystrot.
Syntax: angmax angle
See tilt.
Syntax: centric on/off
With the option centric on in distance refinement, faces related by an
inversion center are refined together.
With the option
centric off, these
faces are refined separately. This option has no influence on the command
filter (point group symmetry) and
on the other refinement commands (volume,
crystrot, tilt, etc.). By default the option centric is set
on,
independent of the supplied point group symmetry.
Syntax: correction ABST/ABSG
The absorption correction procedure ABST or ABSG in PLATON is chosen.
By default the selection is taken from the ins file. Please consult the
PLATON manual for a
detailed description of the differences between ABST and ABSG.
Syntax: extreme f
Sets the initial refinement shifts for
volume and distance
refinements. With a rough starting model this value should be 1.0.
With a good starting model, for example at the end of EUHEDRAL refinements,
the value can be lowered to speed up the refinements.
Syntax: highindex n
Multiply all the face indices by a constant number. The resulting indices
all are less or equal to n.
See tilt. The opposite operation is called
reduce.
Syntax: improve f
Default: improve 0.001
Sets the refinement improvement threshold.
threshold =
(0.1*w1 + 0.5*w2) *
f/1.5
A refinement is considered
to be improved if the final R2 value is lowered by a value greater than
threshold. Used with
volume and distance
refinements.
Syntax: initdistance distance
Set initial distance for adding faces using the commands
addface,
addfacehkl,
addfaceperp,
addfacesum,
bestsphere,
buildcube or
buildsphere.
Default = 0.07.
Syntax: phi start stop delta
Set the default values for a crystrot refinement.
See crystrot,
crystrot1,
crystrotface and
crystrothkl.
Syntax: tol f
Sets the tolerance, when the refinement stops. Lower
values give more accurate results. Default = 0.01
Syntax: weight
w1 w2
Sets sets the weights
w1 and w2 for the R2 calculation.
All EUHEDRAL refinements
of the crystal shape are based on this R2.
R2 = w1*Rint + w2 * Rpsi
Rint = ∑[abs(int - intmean)] / ∑(int) (G.M. Sheldrick: SHELXL)
Rpsi = (1/n) *
∑[(intmax/intmin)-1] (W. Herrendorf: HABITUS)
Defaults: w1=10.0 w2=0.1
With these defaults R2 is approximately 10 times the SHELX Rint.
For a pure SHELX Rint set w1=1.0 and w2=0.0
Refinement commands
All distances of the different crystal faces are refined in one refinement
cycle (simplex algorithm). In contrast to the volume
refinement, the ratio of the distances is allowed to change.
Use distance for a one-by-one refinement
of the face distances.
Syntax: crystrot
phistart phistop delphi angmin
Rotate the complete crystal with respect to 13 rotation axes:
011 101 110
011 101 110
111 111 111
100 010 001
111 (definition in cartesian system).
For each axis, the crystal is rotated from
phistart to
phistop with
delphi steps.
A new orientation is ignored if it is within
angmin degrees of an already generated one.
The crystal shape is held constant during the refinement. Please be
aware that the indices of the
faces may become relatively high numbers, which you may want to
reduce.
Use crystrotsimplex for a simplex refinement of
the crystal orientation.
Syntax: crystrot1
Rx Ry Rz phistart phistop delphi angmin
Rotate the complete crystal with respect to a single rotation axis.
The axis is specified with the cartesian vector
Rx Ry Rz.
The crystal is rotated from
phistart to
phistop with
delphi steps.
A new orientation is ignored if it is within
angmin degrees of an already generated one.
The crystal shape is held constant during the refinement.
Please be aware that the indices of the
faces may get relatively big, which you may want to
reduce.
Syntax: crystrotface
facenumber phistart phistop delphi angmin
Rotate the complete crystal with respect to a face normal.
The rotation axis is specified by facenumber.
The crystal is rotated from
phistart to
phistop with
delphi steps.
A new orientation is ignored if it is within
angmin degrees of an already generated one.
The crystal shape is held constant during the refinement.
Please be aware that the indices of the
faces may get relatively big, which you may want to
reduce.
Syntax: crystrothkl
h k l phistart phistop delphi angmin
Rotate the complete crystal with respect to a reciprocal axis
(see coordinate systems).
The rotation axis is specified by the indices
h k l.
The crystal is rotated from
phistart to
phistop with
delphi steps.
A new orientation is ignored if it is within
angmin degrees of an already generated one.
The crystal shape is held constant during the refinement.
Please be aware that the indices of the
faces may get relatively big, which you may want to
reduce.
Syntax: crystrotsimplex
angle
Rotate the complete crystal with respect to the 3 cartesian
axes (100, 010 and 001). The initial angles along the
3 axes are set with the value of angle.
The crystal shape is held constant during the refinement.
Please be aware that the indices of the
faces may get relatively big, which you may want to
reduce.
Use crystrot for a brute force refinement of
the crystal orientation.
The distances of the faces are refined separately (parabolic refinement). If
the parameter centric is set
on (default), faces
related by an inversion center are refined together, independent of the point group.
The refinement stops if the improvement in R2 is smaller than the threshold
set by improve.
Faces are automatically removed by EUHEDRAL if they don't intersect with the
rest of the crystal. If this results in a lower R2 value, the corresponding face
is permanently removed.
Use amoeba for a simplex refinement
of the face distances.
Syntax: tilt
highindex angmax face1 face2 ....
With the command tilt one or all faces are
tilted with respect to the rest of
the crystal shape. In a first step, the indices of a given face are multiplied
by a
constant number (For example, face (120) becomes (360)). The value of
highindex determines which index value should not
be exceeded by this
multiplication. Then the indices are permutated, not exceeding the value for
"maximum angle", supplied by the program user. The user can indicate, whether
all faces should be tilted or only one face (face number).
Faces are automatically removed by EUHEDRAL if they don't intersect with the
rest of the crystal. If this results in a lower R2 value, the corresponding face
is permanently removed.
After using tilt you may want to use
reduce to obtain nicer face indices.
The distances of all faces are refined together.
The refinement stops if the improvement in R2 is smaller than the threshold
set by improve.
This command can also be used as a test, whether the given crystal shape is reasonable.
If the refinened volume
factor is close to zero, the absorption coefficient might be wrong, or the
crystal orientation is in error. In the latter case you could try
the command crystrot.
Graphics
Set the colours for the graphical display. Default values between [].
- colour axes
-
colours of the coordinate axes. First the foreground
colour, then the background. ["yellow" "yellow4"]
- colour bg
-
colour of the background. ["grey30"]
- colour circle
-
colour of the circles in the filter window ["grey40"].
- colour cosi
-
colour of the incoming beam in the filter window ["green"].
- colour coso
-
colour of the outgoing beam in the filter window ["magenta"].
- colour faces
-
colours of the faces. First the foreground, then
the background. ["orange" "brown"].
- colour fg
-
remaining items (f.e. edges). ["white"].
Continuous rotation of the picture of the crystal shape.
You have to interrupt (control-c) the program to stop this rotation.
Syntax: mode cone/stereographic/ajmd/z
The option mode is active during the
filter procedure.
The incoming and outgoing beam is plotted to allow you to judge, whether the
complete crystal is covered by the selected subset. Different projections
for the plot are possible.
Rotate the picture of the crystal shape 360 degrees.
Related command: partialrot
Partially rotate the picture of the crystal shape.
The rotation angle is set with viewpartial.
Related command: onerot
Syntax: plotaxes on/off
With plotaxes on or
plotaxes off you can decide, whether the
crystal axes are plotted in the
picture of the crystal shape.
Syntax: plotcorner on/off
With plotcorner on or
plotcorner off you can decide, whether the
labels of the corners are plotted in the picture of the crystal shape.
Default is plotcorner off.
Syntax: plotlab on/off
With plotlab on or
plotlab off you can decide, whether the
cartesian axes (diffractometer system) are plotted in the
picture of the crystal shape.
See coordinate systems.
Syntax: pointsize n
With the command pointsize
you can set the size (in pixels) of the
points, which are used for displaying the incoming and outgoing beam during
the filter procedure. Default = 3.
Syntax: posx n
With the command posx you
can set the x position (in pixels) of the
graphical window, which is used for filter,
and the picture of the crystal shape. Zero = Left side of the screen.
Syntax: posy n
With the command posy
you can set the y position (in pixels) of the
graphical window, which is used for filter,
and the picture of the crystal shape. Zero = Bottom side of the screen.
Syntax: size i j
With the command size
you can set the absolute size (in pixels) of the
graphical window, which is used for filter,
and the picture of the crystal shape. Defaults to 1/3 of the screen height.
Syntax: vertical on/off
The option vertical can be set on or
off. With vertical off
the picture of the crystal is displayed with a view along the cartesian z axis. With
vertical on (default) the cartesian z axis is
pointing upwards, simulating
a Nonius KappaCCD microscope view.
See coordinate systems.
Syntax: viewdir h k l
view along hkl direction
(see coordinate systems).
(And remember option vertical).
Syntax: viewpartial angle
Set the angle for partialrot.
Default value is 20°.
Syntax: viewperp i
view perpendicular to face with facenumer i
(and remember vertical).
Syntax: viewrot angle
rotate view vector along the vertical screen axis.
Syntax: viewspeed speed
Rotation speed (degrees/second) for rotating the picture of the crystal in the graphical
display. The default value = 30.
Related commands:
onerot,
partialrot
Syntax: viewxyz x y z
View along a cartesian vector
(see coordinate systems).
(and remember option vertical).
Misc
Syntax: copy name
With the command copy, a new ins file
is created, and reread. Usefull to play around with a model
without losing the original data.
With the command edit, you can edit
the ins file, for example to add or remove
crystal faces. When you use edit
from within EUHEDRAL, all parameters are
adapted automatically. If you edit the ins file with an external editor, you
must explicitely use the EUHEDRAL command readins.
The command edit makes use of the system editor of
the UNIX shell. With the
UNIX command printenv you can check, which system editor is set on your
system. Please consult the manual of your UNIX shell, if you wish to set a
different system editor. If no editor is specified, vi will be used.
Please note that when using the GUI, the editor has to be started in its
own window (e.g. emacs, nedit, xterm -e vi).
See also face to change parameters for a single face.
end program
Syntax: hkl h k l
Display reflection information. Only for debugging purposes.
The option XTAL of the PLATON program is used to display the crystal shape. You
can rotate the crystal to obtain a better view. It is possible to write
postscript or hpgl files. The PLATON options to change the crystal description
should not be used for EUHEDRAL. Please use the edit
command of EUHEDRAL instead.
If possible, a reduction of the face indices is performed. For example, the
face 222 will be transformed into 111. This option is especially useful after
a refinement of tilt or crystrot.
With the command status you can check,
which parameters are currently set in EUHEDRAL.
The command test checks the consistancy of
your description of the crystal shape. It also displays the
surface areas of the different faces and the angles
between them. Maybe you wish to remove faces with only a small surface. For
this you can use the EUHEDRAL commands edit or
deleteface.
Syntax: workfile name
The default names of the workfiles for euhedral are subfile.*. If you want
to change the name you can use the command
workfile.
Syntax: writehkl x y z
write (filtered) hkl file. (This command is used internally by
EUHEDRAL and normally not invoked by the user).
Go to EUHEDRAL introduction.