Toggle for (re)setting the minimum line width for X-Window Graphics Display. This feature
may be useful depending on the default X-server line width.
1.4.9.3 - COLOR Toggle
Switch between Black&White and Color. When RED, hetero atoms are distinguished with a
differing color.
1.4.9.4 - LablHetAts Toggle
Label Hetero Atoms Only Toggle.
1.4.9.5 - DispAllLab
By default, a label will not be drawn for an atom when the automatic positioning function
cannot find a proper place. This Toggle overrules this feature by plotting a label anyway.
The label can then be moved manually to the best alternative position.
1.4.9.6 - LabelCg Toggle
Toggle for the display and inclusion in geometrical calculations of supporting Cg 'atoms'.
1.4.9.7 - Alias Toggle
PLATON sets some restrictions on atom labels. When a label is given in a CIF that conflicts
with those rules, an alias (terminated with a #) is generated. By default, the original labels
are presented on output and graphics where ever possible. With this toggle ON (RED), the
aliases used in PLATON are given.
1.4.9.8 - MolFit by Clicking
A Quaternion based fit will be done of molecule #1 on molecule #2 (or molecule #n on
molecule #m for that matter). Both molecules in the asymmetric unit to be fitted will in
general be chemically equal. However, by special arrangement, unequal molecules may be
fitted as well (usually in the form of two concatenated 'PDB-style' datafiles as input).Atoms
to be used for the fit (at least 5 pairs) should be clicked in pairs. The Fit sequence starts and
ends by clicking on the menu-item
FITbyCLICK. Note: Clicking on just two
corresponding atoms will suffice in cases where the atom labels in both residues to be fitted
are such that they are pairwise equivalent after sorting. For more information on molecule
fitting see
FIT
and
AUTOFIT
. There are three click positions. The middle click position
attempts the best fit of molecule #n on molecule #m. The right click position attempts the
best fit for inverted molecule #n on molecule #m. The Left click position attempts the fit of
molecule #n and inverted molecule #n on molecule #m respectively, keeping the best fit.
1.4.9.9 - AUTO MOLFIT Toggle
A (Quaternion based) fit will be done of molecule 1 on molecule 2. Both molecules should
be chemically equal. For more information on molecule fitting see
FIT
and
AUTOFIT
. The
Left click position attempts the best fit including inversion.
1.4.9.10 - (UAE)WLSPL
The default weighting of atoms determining the least-squares planes is UNIT. Alternatives
are weighting based on Atomic weight or s.u.
1.4.9.11 - Angle2Lines
Option to calculate the angle between two lines by clicking on two pairs of atoms.
1.4.9.12 - LstRadBonds
(To be done)
1.4.9.13 - LIST CELL/SYMMETRY
Left Box: List current cell dimension info. Right Box: List current space group symmetry
option.
1.4.9.14 - LIST ATOMS & UIJ
Left Box: List atomic positions and related data for inspection. Right Box: List UIJ- main
Axes + U(eq).
1.4.9.15 - LIST FLAGS & RADII
Clicking in Left Box: List of internal FLAGS for inspection. Clicking in Right Box: Listing
of JOIN radii used for inspection .
1.4.9.16 - LIST ARU
List asymmetric residue codes (ARU) on alphanumeric window. This feature is useful to
find out about the applied symmetry operations on atoms that are shown with a symmetry
code extension on the plot.
1.4.9.17 - DISPLAY BY RESIDUE
This button contains NRES (= number of species) + 1 clickable boxes. By default, all
residues are drawn. This corresponds to the leftmost click position. The other click positions
bring up individual residues. The number of the residue displayed is shown on the drawing.
The number 0 indicates that all residues are shown.
1.4.9.18 – Reverse B&W
Change background from black to white. This option may be useful for screen captures of
images to be printed.
1.4.9.19 - STEPWISE ROTATION ABOUT Z
Stepwise rotation about Z (perpendicular to image). Step size and direction based on click
position.
1.4.9.20 - STEPWISE ROTATION ABOUT Y
Stepwise rotation about the horizontal axes (Y). Clicking in the central area gives small
rotation steps. Clicking further from the center corresponds with larger rotation steps.
Clicking left from the center or right from the center determines the sense of rotation.
1.4.9.21 - STEPWISE ROTATION ABOUT X
Stepwise rotation about the horizontal axes (X). Clicking in the central area gives small
rotation steps.Clicking further from the center corresponds with larger rotation steps.
Clicking left from the center or right from the center determines the sense of rotation.
1.4.9.22 - LtReference
(to be done)
1.4.9.23 – LsplWithEnd -Interactive calculation of dihedral angles between least
squares planes.
The Plane definition of the first plane starts with clicking on the
Lspl button followed by
clicking on the atom centres of the atoms participating. This first sequence is terminated and
the sequence for the second plane started by a click on
With. The second sequence is ended
(and the calculation initiated) by clicking in the
End field. Alternatively, an instruction
similar to
LSPL c3 c4 c5 WITH c1 c2 c6 could be issued from the keyboard. Atoms are
treated with unit-weight by default. Alternatives are weighting based on atomic weights and
standard deviations (esd, su). The weighting scheme may be changed using the
(UAE)
WLSPL button.
1.4.9.24 – LsplDistEnd - Interactive calculation of least squares planes.
The Plane definition starts with clicking on the
Lspl button followed by clicking on the
atom centers of the atoms participating. The sequence is ended (and the calculation initiated)
by clicking in the
End field. Plane determining atoms may be separated from those for
which the distance to the plane only has to be calculated by clicking on the
Dist field
between the clicks on atoms. Alternatively, an instruction similar to
LSPL c3 c4 c5 DIST c1
could be issued from the keyboard. Atoms are treated with unit-weight by default.
Alternatives are weighting based on atomic weights and standard deviations ( s.u.). The
weighting scheme may be changed using the
(UAE)WLSPL button.
1.4.9.25 - PLUTON & END BUTTONS
Clicking on the PLUTON button provides a direct pathway to PLUTON sporting the same
connectivity and orientation etc. Return to main PLATON menu with 'END'.
1.4.10 – PLATON SUB-MENU #0
1.4.10.2 - NOMOVE Toggle
The NOMOVE toggle is designed to give some global control over the moving (with the
application of an allowed symmetry operation) of atoms into a connected set (i.e. molecular
species, with their centers of gravity within the unit cell range) from an input set of
coordinates. When active (indicated by a RED menu-item NoMove) coordinates are not
transformed (moved) from their input positions. Rather, new symmetry related positions for
atoms connected to the starting set are added. Unwanted results and side-effects may be
obtained when the underlying connectivity assumption is false. The
NOMOVE option is
ON by default for CIF and FDAT Input data, assuming a connected set. If the molecules are
none-the-less not connected an undesirable connectivity may result. Set
NOMOVE OFF
when the input coordinate set does not form a connected set. This is the default (assumption
) for non-CIF or non-FDAT data sets (i.e.
shelxl.res or
.spf files). A more detailed control is
available via the TRNS instructions (see
Section 2.4.1). The best approach to a connected
set is to handle this issue at the
.res (i.e. structure solution) stage.
1.4.10.3 - Join-Expand
