Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht

9.3 PLATON - ANALYSE Menu

 

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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

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9.3 PLATON - ANALYSE Menu

 

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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'

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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.

4.17 PLATON/ORTEP (Sub) Menu Options

The following options are available from the Ortep Menu (Red = Active)

ToOptions   - Path to a sub-menu

StereoOpts  - RedGreen and BlueGreen Stereo (Alternative = Mono) 

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