WinGX v1.64
Chapter. 9.3 PLATON
19
CELL 0.71073 10.1 10.2 10.3 90 90 90
LATT P C
SYMM -x, y, -z
MULABS 6.5 0.3
MULABS without parameter data gives a correction without the theta dependence (i.e.
average value = 1.0). Parameters may be set interactively with MUMM (for mu in mm) and
RADIUS (mm) instructions. The MULABS implementation of the Blessing Algorithm is
EXPERIMENTAL and may change somewhat on the basis of future experience. MULABS
can also be called from the main PLATON menu (MULABS button) In that case leave out
the MULABS line from name.ABS file. MULABS should be useful in particular for
redundant data sets collected with area detectors (e.g. KCCD). However it can be also useful
for redundant datasets originating from serial detector diffractometers.
Note: This implementation is independent of the particular brand/type of diffractometer used;
all information needed is included in the (SHELX-style) direction cosines (apart from the cell
dimensions and Laue symmetry). A new file name.HKP is written (SHELX HKLF 4 style)
implementing the absorption correction. Some additional information is written to name.LIS
4.9 Psi-scan based absorption correction
PLATON/ABSPSI for psi-scan based absorption correction requires two files
1. a reflection file (SHELX HKLF 4 + Direction Cosines) : name.HKL
2. an instruction file : name.ABS
The content of the instruction file should look like
TITL S588A
CELL 0.71073 11.1364 12.0577 15.3782 90 90 90
ABSP
The SHELXL .HKL file should contain two sections, separated by a blank line. The psi-scan
data should go in the second section. Such a file is produced for CAD4 data using the data-
reduction program HELENA. Each psi-scan set should consist of 36 measurements, measured
in 10
o
steps.
4.10 Xtal-Plot
The face indexed absorption correction options contain a feature to draw crystals for checking
the correctness of the description that can also be used stand-alone. The essential input file
name.INS should contain
TITL
CELL
FACE h k l dist
.....
FACE h k l dist
It may be invoked from the main PLATON menu (ABSTOMPA). Planes may be added,
modified or deleted interactively.
4.11 Residue Numbers in PLATON and PLUTON
PLUTON & PLATON use different algorithms to assemble residues, resulting in differing
assigned numbers. In order to get consistent residue numbering, PLUTON should be run
through PLATON (PLUTONauto button). PLATON will than generate a name.ELD file with
WinGX v1.64
Chapter. 9.3 PLATON
20
the order and numbering of residues as in PLATON. This feature is call the 'PLATON
Compatibility mode'
4.12 Atom renaming in PLUTON (.res files).
PLUTON can be used for interactive atom renaming. A new file (.new) including changes is
written only under certain conditions:
• PLUTON should have been called directly from the command line, either via an alias
'pluton' or 'platon -p' or via the 'toPLUTON' option in the PLATON opening menu. The
PLUTONauto button will not work because the derived name.ELD will be read, rather
than the name.RES file
• The input file must be recognised as 'shelx.res' format type.
There are two options for RENAME
1. KEYBOARD
• REN C100 C1 C150 C2 C5 P1
• This will change C100 into C1 etc.
2. VIA MENU: Click in CONTENT MENU on RENAME ATOM
• Click on ATOM to be renamed and give new name via KEYBOARD
4.13 Default instructions for PLUTON
PLUTON (i.e. the PLUTON path through PLATON) starts to read data from an input file
(e.g. name.RES ). That file usually, but not necessarily, contains the pertinent data for the
structure only. Before switching to interactive input (console or menu) a file named
name.DEF is read. This file may be used to execute a number of instructions before the first
plot.
Example of name.DEF
STRAW COLOR
LABEL
PLOT
Such a file is generated automatically when PLUTON is run in the PLATON-compatability
mode via the PLUTONauto button.
4.14 Graphics (Meta, POVRAY, RASMOL)
PLATON will generate by default a PostScript file of the image displayed on the screen by
clicking on the 'EPS' button. The PostScript default may be changed into HPGL or TEK4014
with a button on the PLATON opening window. In the PLUTON mode, there are two
additional graphical interfaces.
1. clicking on 'Pov' will generate a file name.POV suitable for the raytracing program
POVRAY. POVRAY will be executed when implemented.
2. clicking on 'Ras' will generate a 'PDB' tructured name.RAS file suitable for the molecular
visualisation program RasMOL. RasMOL will be executed when implemented.
The executables 'povray' and 'rasmol' are assumed to be globally accessible. Alternatively, a
path may be given in environment variables.
e.g. 'setenv POVEXE '/usr/local/bin/povray'
'setenv RASEXE '/usr/local/bin/rasmol'
9.3 PLATON - ANALYSE Menu
WinGX v1.64
Chapter. 9.3 PLATON
21
4.15 Output Listings .lis & .lps (Print & View)
PLATON produces a detailed 132 column listing file (line printer ASCII format) on a file
with extension '.lis' in addition to the limited (80 column) listing that is sent to the display
window from which the program was invoked. The listing file can be printed or read by a
post-processing program to extract relevant data from it. The .lps file contains the same
information as the .lis file but now in EPS-format. This file may be either sent to a PostScript
printer or viewed with programs such as ghostview. Generation of the '.lps' file can be
suppressed by clicking on the 'EPS-Listind' button in the PLATON-Opening menu.
4.16 PLATON Main-Menu Options
The following options set special features: RED when active !
To Pluton - Direct path to PLUTON function (Native-mode). Symmetry
codes may be inconsistent with those in PLATON.
Nomove - Coordinates are not transformed from input positions.
This option is ON by default for CIF-Input data, assuming a
connected set. Set 'Nomove' OFF when coordinates do not form a
connected set.
AtomSort - By default, the atom list is sorted on atom type and numerical
value in the label.
Organic - Different Radii are used for Organic/Inorganic Structures
Round - By default, Coordinates and derived data are rounded following
the 1-19 rule.
Parentheses - By default, the numerical part of the label is enclosed in
parentheses.
Nosymm - When Active, No symmetry is applied.
R/S-Determ - R/S-Determ is enforced when active.
SHELXL ATWT - Mol.Weight data 'as-in' SHELXL
Norm H-Bond - X-H distances are normalised to standard values
Save-InstrS - Toggle for saving instructions
Print-Level - (Not completely implemented yet)
Click on leftmost position results in no listing file and
on the rightmost one a full listing on '.lis'.
EPS-Listing - Toggle to switch off the generation of a PostScript version
on '.lps' of the '.lis' file.
EPS HGL TEK - Default setting of the graphics output (PostScript, HP-GL or
Tektronix 4014) on the Meta-file.
Auto-Plot - New Plot on new instruction (on/off) toggle.
Menu-off - Keyboard input only. Type 'MENU ON' to return to menu-mode.
The following options are available from the Ortep Menu (Red = Active)
ToOptions - Path to a sub-menu
StereoOpts - RedGreen and BlueGreen Stereo (Alternative = Mono)
Dostları ilə paylaş: |