WHAT IS PLATON AND HOW TO GET STARTED


PLATON (C) 1980-2017 A.L.Spek, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.


WHAT IS PLATON ?

PLATON is a versatile SHELXL compatible multipurpose crystallographic tool.

Most PLATON features complement those available in the excellent and widely distributed SHELX2016 package for crystal structure determination and refinement.

Historically (1980) PLATON started out as a program for the automated calculation of derived geometrical data (i.e. bond distances, bond angles and torsion angles, including su's (esd's)) for structures refined with SHELX76. Since then, that basic function evolved into an automatic function to calculate everything of possible interest (both intra- and intermolecular)for a given structural parameter set (Instruction: CALC).

Over time, various other tools were introduced (Molecular Graphics i.e. PLUTON & ORTEP, Absorption correction, Data Validation etc.), some of which requiring a reflection datafile as well.


PLATON HAS MANY FACES

PLATON comes with at least six different faces, depending on the way the program is invoked.
  1. PLATON. The molecular geometry tool.

    This is the (generic) native mode when the executable is invoked as platon

  2. PLUTON. The molecular graphics tool.

    This mode is entered, as opposed to through a platon option, when invoked (via a softlink to platon) as pluton or (with the command line option '-p') as platon -p

  3. SYSTEM S. The crystallographic supervisor shell.

    This mode is entered when invoked (via a softlink to platon) as s or platon -s

  4. CIFCHK. The CIF Validation tool.

    This mode is entered when invoked (via a softlink to 'cifchk') as cifchk or as platon -u

  5. HELENA. Data reduction (i.e. generation of 'shelx.hkl') from raw CAD4-data.

    This mode is entered when invoked as helena or platon -k

  6. STIDY. Standardisation of inorganic structural parameters following Parthe & Gelato.

    This mode is entered when invoked as stidy or platon -Y.

Note: introduce link ln -s platon pluton for direct access to PLUTON etc.


WHAT DOES PLATON OFFER

PLATON implements the following features:

Note: Most PLATON features are currently available only for non-protein structures.

Depending on the desired type of calculations PLATON requires, similar to SHELX97, two ASCII files (vide infra):

  1. a coordinate (instruction) file (CIF,PDB,RES.FDAT,SPF)
  2. and optionally a reflection file.(HKL,FCF)

WHAT COORDINATE DATA INPUT STANDARDS ARE ACCEPTED

Parameter data may be given in various formats that are in common use including

Example data sets are given in parentheses. Note: there are some restrictions on atom labelling (A4).

A CIF file is recommended when su's (= e.s.d.'s) on the derived geometry parameters are desired. (see examples)


REFLECTION FILE DATA FORMATS

Reflection data should be provided in the SHELX format (optionally with SHELX76-style direction cosines.
Some program options also accept SHELXL97-style FO/FC CIF's as reflection input.


HOW DO I GET A COPY OF PLATON


MENUS, MOUSE CLICKING and KEYBOARD


INTRODUCTORY PLATON TUTORIAL

A Sample run of the program (with the test data on sucrose.spf, to be copied as well) is done with the command line:

platon sucrose.spf or platon -o sucrose.spf

followed by the interactive instructions (on the program prompt >>):

>> CALC

(or click on 'CALC ALL')

This will give an exhaustive geometry analysis. The main results are on the listing file to be printed on an (ascii) lineprinter (Some summary information is also directed to the display).

alternatively, the instruction (after restarting the program):

>> CALC ADDSYM

will provide a test for missed symmetry (cf. the LePage MISSYM (C) algorithm), or:

>> CALC SOLV

will do a calculation to identify missed solvent areas or

>> TABL ACC

will generate a file as a starting point of a CIF-file suitable for submission to Acta Cryst C.

A default labelled ORTEP is produced with:

>> PLOT ADP

The SQUEEZE filter needs two inputfiles: 1) a shelxl.hkl (HKLF 4) reflection file and 2) a shelxl.res file containing the current refined parameter set (excluding atoms modeling the disordered solvent area). The calculations are done with the instructions

>> CALC SQUEEZE

A file named shelxl.hkp contains a new reflection file where the disordered solvent contribution is substracted from the observed data. Further refinement can be done against this new file.

** Note: The SQUEEZE filter has been used succesfully for structures
         containing disordered toluene or similar molecules. Experience
         is still building up and there is no quarantee that the program
         will do the right thing on unfamiliar terrain (in particular
         additional disorder in the discrete structural part has to be
         sorted out for their effect on the solvent area).   

         See also How_to_use_SQUEEZE

See also the Web-Pages:

PLATON/ABSCOR-Manual (Absorption Correction)

PLATON-Manual

PLUTON-Manual


RECIPROCAL LATTICE SYMMETRY


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.

There are three ways to run the PLUTON option within PLATON

1 - with the '-p' option on the command line

e.g. 'platon -p sucrose.spf'

2 - with a 'softlink' of 'pluton' to the 'platon' executable:

i.e. 'ln -s platon pluton'

sothat PLUTON can be invoked as usual: 'pluton sucrose.spf'

3 - the PLATON instruction 'PLUTON' (or clicking on 'toPluton')

Note: 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.


GRAPHICS

Various graphics standards are supported including X-Window, HP-GL, Tek4010, PostScript (Also suitable for MacUsers).

When graphics is invoked with a PLOT instruction, X-window graphics is attempted. When the software cannot connect to the X-server (check for appropriate 'xhost' and 'setenv DISPLAY' instructions), it automatically switches to the low level TEK4010 graphics mode which may be appropriate for use on PC's running a terminal emulator (I use PC-PLOT) connected to the host computer (e.g. by a phone line).

Conversion of different image formats can be performed with ImageMagic available from http://www.wizards.dupont.com/cristy


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)).

Postscript files can be printed on non-postscript printers with the programs ghostscript and ghostview, available from http://www.cs.wisc.edu/~ghost


RAY-TRACED AND RASTER MOLECULAR GRAPHICS

POVRAY

High quality (color)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 '.pov' file with the current content, style and orientation of the current PLUTON-display.

POV-Ray (information) may be obtained from:

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


RASTER3D

Rendered ORTEP presentations may obtained through PLATON using raster3d

Note: a tiff-file is produced. An attempt is made to display this file either with xv, gimp or display software.


RASMOL

Access to RASMOL through PLATON/PLUTON is available by implementing rasmol


CIF-VALIDATION


CONCLUDING REMARKS


Prof. Dr. A.L. Spek (Emeritus)
Bijvoet Centre for Biomolecular Research
Vakgroep Kristal & Structuurchemie
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands. Email: a.l.spek@uu.nl
WWW : http://www.platonsoft.nl/
WWW : http://www.platonsoft.nl/platon/


PLATON HOMEPAGE


22-Feb-2017 A.L.Spek