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

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This should be done in a separate PLATON run. You will need SHELXL files name.INS and

name.HKL (HKLF 4 - with direction cosines in the SHELX-76 style - their validity is

checked. A DELABS run may be done (when applicable) on the reflection file modified by

SQUEEZE.

NOTE  Be aware of the fact that the use of DELABS/DIFABS as an empirical absorption

correction technique is considered to be 'sloppy crystallography' by some

crystallographers/referees/journals. This implementation attempts to avoid possible human

errors due to (or related to) cell transformation matrices, scaling factors, anisotropic

displacement parameter model etc. 

1.5 Analytical absorption correction

For those having crystals that can be face-indexed there is the easy-to-use implementation of

the de Meulenaar & Tompa absorption correction method. This filter may be invoked with:

                 PLATON name.ABS

again, you will need a SHELX name.HKL file including the direction cosines The file

name.ABS should contain:

TITL text

CELL lambda a b c alpha beta gamma

FACE h k l d 

......

ABST mu

The d-values are the distances of an arbitrary point within the crystal to their corresponding

faces. d & mu should be given in mm.

1.6 Reciprocal lattice symmetry

The symmetry of the reciprocal lattice at hand may be inspected with the PLATON/ASYM

utility for a given SHELX .HKL

1.7 Program PLUTON

The previously available stand-alone molecular graphics program PLUTON is now available

as an option within PLATON. The original PLUTON is now obsolete and no longer

supported & maintained. Clicking in the main PLATON-MENU on the button PLUTON will

result in a PLATON-run to generate an input file for PLUTON to make both  consistent.

1.8 Window Menu

1.8.1 PLATON

By default, a menu is shown from which the desired options can be MOUSE-CLICKED.

Traditional keyboard entry is possible either through the 'MenuOff' button.

1.8.2 PLUTON

By default, a PLOT instruction will bring up the Window Menu from which mouse-driven

options may be run. The more complex instructions may be given via the keyboard. The

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menu-feature is switched off either through a menu option or with the instruction MENU OFF

(to be given before the first PLOT instruction).

1.9 Hard-copy graphics

Hard copies of the current display are conveniently obtained as a (meta) file by clicking on

the 'Meta' option. By default, a PostScript file (Landscape Mode), suitable to be sent to a

PostScript laser printer will be produced. Alternatively, the instruction 'SET META HPGL'

will make the default HPGL (suitable when graphics is to be included in a wordprocessor

environment (e.g. WordPerfect)).

1.10 Ray-traced molecular graphics

High quality (colour)graphics is easily obtained with the excellent Public Domain package

POV-Ray. The required input files for that program are conveniently generated using the

'POV' button in the PLUTON menu. This will generate a  name.POV file with the current

content, style, colour and orientation of the current PLUTON-display.

POV-Ray (information) may be obtained from:

http://www.povray.org  and ftp.povray.org.

 1.11 Printing

PLATON generates an extensive listing file name.LIS that can be viewed with an editor,

listed on a lineprinter or sent (via a filter) to a laserprinter. A utility that can be used for this

purpose is 'pstext' (available in directory 'util' as 'pstext.shar.z'). An ASCII text is converted

into a PostScript file. We use: 'pstext -s 9 -l -i 15 -2 platon.lis | lpr -Ppostscript' to print the file

'platon.lis' on out HP-postScript laser printer.

1.12 CIF-validation

PLATON can be run in a special mode to provide some validation checking of CIF's. It is still

experimental with  criteria not necessarily final. Most warnings can be signs of unresolved

problems that should be looked at more closely and at least discussed in the experimental

section of the paper when sent for publication. See Section 9 below for further details

1.13 Miscellaneous

Further information on available instructions is obtained with the instruction: 

HELP

A right mouse click on the menu launches the hypertext help facility with a direct connection

to the PLATON home site at:    http:/www.cryst.chem.uu.nl/platon/pl000000.html

2. On the internal workings of PLATON

This section provides a framework to understand the effects of the various available

instructions. 

 

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The input atomic coordinates (X, Y, Z) are with reference to user-defined axes (a, b, c), which

will usually be either crystallographic unit cell axes or an arbitrary orthogonal set; these

coordinates are input as fractions of the unit cell edges or as Å units (in the latter case they are

converted and stored as fractions of dummy cell edges). A second, orthogonal

system (A, B, C) with coordinates (XO, YO, ZO) in Å’s is set up internally (see J.D. Dunitz,

X-Ray analysis and structure of Organic molecules, p236): A is a unit vector along a, B is a

unit vector normal to a in the ab-plane, and C is normal to A and B. B will coincide with b in

monoclinic cells in the b-setting. If the input axes are orthogonal, the two sets of axes a,b,c

and A,B,C are coincident. The third system is the plotting coordinate system in cm: XP across

the picture from left to right, YP up the picture from bottom to top and ZP out of the paper.

All these axial sets are right-handed and absolute configuration is preserved in all rotations. 

As atoms are input to the program, they are stored in the X,Y,Z and XO,YO,ZO axes systems.

Each atom also has additional information stored for it such as estimated standard deviations,

thermal motion parameters, a name (the embedded element name is used by default to set

various radii to be used during the subsequent calculations) and various bit flags such as the

inclusion bit. Coordinate data are checked for duplications on input. Atom labels not

conforming to the required format are renamed. 

A CALC instruction generally initiates a distance search on the basis of the previously set or

supplied radii. In the INTRA mode this results in the set-up of an array that stores per atom all

connections that are found. This list is used subsequently by a geometry listing routine that

generates all unique bond distances, bond angles and torsion angles. Simultaneously with the

set-up of the connectivity array all atoms are transformed (when necessary) to obtain a

connected set. In addition, in the case that the molecule lies on a special position, the primary

coordinate list is expanded with additional symmetry generated atoms in order to handle the

geometry of the complete molecule. See also Section 4 Terms & Notions.

3. Summary of keyboard commands for PLATON

This Section provides a description of the keyboard commands which were available in

PLATON92. Most are still available in current versions (which have a much larger number of

options), though there may be alternative ways of doing things, in particular using the

Window Menu. The full current manual is available in HTML format from

http:/www.cryst.chem.uu.nl/platon/pl000000.html

Commands are grouped together as compound specific, calculation, plot, list and general

instructions. The logical order of calculations is intra-molecular, inter-molecular and co-

ordination geometry.

In the description of individual instructions below the following applies:

•  (Sub)keywords are in uppercase and user data in lower case

•  Data in parentheses are optional.

•  Choices are separated by a slash.

•  Parentheses in atom names (on input) are ignored except for that Ag denotes the atom type

and Ag() the individual atom.

•  Lower case input is automatically converted to upper case.  

•  Lines with a blank character in position 1 are ignored. 

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