The platon crystallographic package - səhifə 24
expressed in an orthogonal Angstrom axial system.
188.8.131.52 – CIF2SHELXL – Convert CIF&FCF to SHELX .ins & .hkl Input Files
This tool converts the data in
name.fcffiles into a
name_shelxl.hklfiles ready for re-refinement with SHELXL. The source data can be those
archived and downloadable for Acta Cryst. C & E papers. This option allows for a detailed
analysis of issues not addressed in the original paper or for the testing of new software. The
name_shelxl.insfile might need some editing in cases where constraints or restraints are
needed. The corresponding keyboard instruction is
CIF2SHELXL. The equivalent filter
operation as a terminal window command line :
platon -H name.cif.
1.4 - PLATON PACKAGE SUBMENU'S
This section gives details for the various submenu options. The coding of the subsections is
nis the submenu number in the top right box of the display and
number (1 to 25) of the box.
1.4.1 - ORTEP TOOL SUB-MENU #0
184.108.40.206 - MONO/STEREO Option Toggle
Clicking in the left box gives
RedGreen Stereo. Clicking in the right box gives
Stereo. Clicking in the same box again will result in the
Monodisplay mode. These options
are available only from this menu.
220.127.116.11 – Hydrogen Atoms INCLUDE/EXCLUDE
Hydrogen atoms are included (RED) or excluded from the ORTEP plot by left-button
clicking on the
(include/no)H-atombutton toggle. Individual H-atoms can be made
immune for the global effect of the H-atom toggle with the HINCLUDE/HEXCLUDE
Section 18.104.22.168).This feature can be useful when only a few H-atoms of
interest are to be shown with all others left out.
22.214.171.124 - DeleteAtoms
Click on the centers of the atoms to be removed from the ORTEP display. Note: Atoms
deleted in this way will be ignored in a subsequent SOLV/PLOT (see
calculation but included in the molecule display.
126.96.36.199 – Probability Level
Displacement ellipsoid surfaces can be drawn at probability levels from 10 to 90 % in steps
of 10%. The actual value depends on the click position and shown in the upper right corner
of the display. The default setting is 50%.
188.8.131.52 – Calc Coordination
Click on an atom for the calculation of its coordination geometry. A coordination listing will
be displayed on the graphical window. Clicking on an entry will bring up a display of both
the starting molecule molecule and that of the selected contact. In this way the display of a
selected set of ARU's can be buildup.
184.108.40.206 – Distance Angle and Torsion Calculation
Interactive distance and angle calculation by clicking on the relevant atom centers. The click
position in the sub menu determines whether a distance, a bond angles or a torsion angle is
to be calculated. The option is switched off by clicking again in the same box.
220.127.116.11 - JOIN and DETACH Toggle
Toggle for 'clickable atom' JOIN, JOIN DASH and DETACH operations. This feature may
be useful for changing some bonding details. This function is relesed by clicking in the
same box again. Related keyboard instructions are:
JOIN at1 at2 NODASH/DASH/LDASH(see
Section 18.104.22.168) and
DETACH at1 at2(See
22.214.171.124 - DefineToEnd
With this option, a set of bonds originating from a central atom to selected atoms will be
replaced by a dash line to the corresponding centre of gravity. In general, this function will
be used for bonds between a metal and atoms partaking in a unsaturated system (e.g. a C=C
1. Click on the 'Define' menu box.
2. Click on the base atom (in general a metal)
3. Click on the atoms determining the centre of gravity to which a substituting dashed
bond has to be drawn.
4. Click on the 'End' field.
Alternatively issue the keyboard instruction:
DEFINE at1 TO at2 at3 at4 at5
126.96.36.199 - View Options
The starting orientation (to be refined by rotation instructions) is determined by the click
1. All angles zero
2. Minimum overlap VIEW
3. VIEW down XO
4. VIEW down YO
5. VIEW down ZO
188.8.131.52 - NO DISORDER Toggle
Toggle for the Display/Not Display of major/minor disorder. Left clicking gives the major
disorder form and right clicking the minor disorder form. Clicking in the same box will
bring the display of both back.
184.108.40.206 - LABEL PLOT Options
Global label on/off toggle. Left position for non-hydrogen atoms only. Right click position
includes H-atom labels in plot.
220.127.116.11 - MOVE LABEL Toggle
When active (RED), atom labels may be moved to a new position. Clicking on the lower left
corner of a label will delete the label to appear again at the click position of a second click.
18.104.22.168 - LABEL SIZE
The label size can be globally changed as a function of the click position.
22.214.171.124 - DELETE LABEL Toggle
Individual labels can be deleted by clicking on them.
126.96.36.199 - INCLUDE LABEL
Deleted labels (shown in red) can be reinstated by clicking on them.
188.8.131.52 - Display by Residue
This button contains NRES (= number of residues) + 1 clickable boxes. By default, all
residues are shown. 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. Alternatively, residue #10 will be
displayed with the keyboard instruction
184.108.40.206 - Continuous Rotation
Continuous rotation about the vertical y-axis with speed corresponding to click position.
Rotation can be discontinued by clicking on the image. sim
220.127.116.11 - Stepwise Rotation About Z
Stepwise rotation about Z (perpendicular to image). Step size and direction based on click
18.104.22.168 - 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.
22.214.171.124 - 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
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