The platon crystallographic package - səhifə 59
and is useful as a preliminary run for checkout and to find a good view direction.
Note: since atoms are represented by points in this presentation, as are bonds when viewed
along their direction, non-bonded atoms and some linear molecules viewed from the end are
not shown in STICK plots.
3.6.73 - STRAW (NUCL/SHADE (a1 a2 (d))/COLOR (a1 a2 (d))/NET (nh nv)/
3.6.74 - STOP
This gives an immediate EXIT from the program.
3.6.75 - TITL text
The title of the plot is normally taken from the TITL card that preceded the coordinate data.
It can be overruled with a new TITL instruction.
3.6.76 - TORSION atom-name1 atom-name2 atom-name3 atom-name4
The dihedral angle (not necessarily involving bonded atoms) for the specified atoms is
calculated as an aid to analyze the geometry of the structure (exhaustive geometry listings
may be obtained with the companion program PLATON).
TORSION C(2) O2 N(2) C(4)
3.6.77 - UNITCELL (OFF/ON) (rbo nli)
This allows a unit cell outline to be drawn. The outlines are treated as bonds (in terms of
radius and number of lines drawn on the bond).
Their default setting is:
rbo= 0.01 and
3.6.78 - UNLABEL (atom-names/atom-types/ALL/(UNITCELL) (ATOMS) (ARU))
This instruction may be used to unlabel. see LABEL.
3.7 - VIEW INSTRUCTIONS
A great variety of instructions is available for the specification of the viewpoint. By default
a minimum overlap instruction (VIEW MIN) is executed (i.e. projection on the molecular
least squares plane). Other instructions allow the view direction to be chosen by the user in
terms of crystal or orthogonal axes, in terms of molecular features, by rotation about the
plotting axes from a previously defined view, by rotation about any other line or bond from
a previously defined view.
3.71 - VIEW MIN (rotations)
This produces a minimum overlap view. The view is perpendicular to the least-squares plane
through the included atom set as generated for the current ARU list. A VIEW MIN
instruction is executed automatically with a PLOT instruction when no previous VIEW
instruction was given.
VIEW MIN XROT 45
3.7.2 - VIEW UNIT (rotations)
This produces a view with XO along XP (horizontal) and YO along YP (vertical), possibly
modified with a sequence of rotations.
A given orientation may be reconstructed, independent from its history, using the three
rotation values that are shown in the lower right corner (xr), the upper left corner (yr) and
the lower left corner (zr) with the instruction:
VIEW UNIT XROT xr YROT yr ZROT zr
VIEW is equivalent with VIEW UNIT.
3.7.3 - VIEW CURRENT (rotations)
This instruction updates the current view matrix. VIEW rotations is equivalent with VIEW
VIEW CURRENT XROT 45 ZROT -60
Note: XROT 45 is a shortcut equivalent for VIEW CURRENT XROT 45
3.7.4 - VIEW XO/YO/ZO (rotations)
View along one of the orthogonal axes towards the origin.
3.7.5 - VIEW AFACE/BFACE/CFACE (rotations)
For a view along the line from the point (1.0, 0.5, 0.5), (0.5, 1.0, 0.5) or (0.5, 0.5, 1.0)
towards the origin (crystal coordinates).
3.7.6 - VIEW ALIGN atom-name1 atom-name2 (aru) WITH XP/YP rotations
This causes an automatic ZROT sufficient to bring the projection of the line between the
two atoms parallel to the plotting XP (YP) axis. A warning message is issued when the two
atoms are superimposed in the current view, so that this instruction is not uniquely defined.
VIEW ALIGN C1 C2 WITH YP
Note: to bring the vector between the atoms atom_name1 and atom_name2 parallel to XP
use the instruction VIEW LINE atom_name1 atom_name2 YROT 90
3.7.7 - VIEW DIRECTION x y z (rotations)
This defines a view along the line from the point (x,y,z) towards the origin (crystal
coordinates). This may be useful for views down the crystal axes for non-orthogonal crystal
3.7.8 - VIEW LINE atom-name1 atom-name2 (rotations)
The direction of view is from the first atom to the second.
3.7.9 - VIEW BISECT atom-name1 atom-name2 atom-name3 (rotations)
The view is into the angle n1-n2-n3 with n2 deepest in the plot.
3.7.10 - VIEW PERP atom-name1 atom-name2 atom-name3 (rotations)
The view is perpendicular to the plane containing the three atom
s, seen from the side which
makes a clockwise order of the atoms in the plot n1-n2-n3.
3.7.11 - VIEW INVERT (rotations)
An inverted image with respect to the current image is obtained with this instruction.
3.7.12 - VIEW MATRIX r11,r12, .. ,r33 (rotations)
This option allows direct input of the view rotation matrix (by row), if it has been
previously calculated by another program. An error message will be produced by a matrix
for which the determinant is not within reasonable rounding errors of +/-1.
(XROT xr)(YROT yr)(ZROT zr)(LROT lr x y z)
(OROT or x y z)(PROT pr x y z)
(BROT atom_name1 atom_name2 br)
Examples of VIEW instructions:
VIEW AFACE ZROT 15
VIEW DIRECTION 0.25 0.25 1
VIEW LINE PT1 BR1
VIEW BISECT C1 C2 C3
VIEW PERP N1 CU1 N2
VIEW LINE C1 C2 ZROT 90 YROT -30
VIEW CURRENT BROT C1 C2 -45
3.8 – Input Parameter File Standards
The atomic parameters (including unit cell parameters, symmetry and coordinates) for a
given structure may be entered in one of the following styles:
- The STANDARD PARAMETER FILE Format (SPF)
- SHELXL-97 and SHELXS-86 type Format (RES)
- Simple Angstrom data format
- The CIF-style (CIF)
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