WHAT IS PLATON AND HOW TO GET STARTED

Most PLATON features complement those available in the excellent and widely distributed SHELX97 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.

Several functions in PLATON (e.g. SPGR and EXOR) are there to implement calculations needed for datareduction, structure determination and refinement with a program system called 'SYSTEM-S' (A crystallographic shell, automating and managing the complete structure determination process in a UNIX environment)

Currently, SYSTEM-S constitutes one of the build-in pathways through PLATON.

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.

• A large variety of standard geometrical calculations, either fully automatic or as specified in detail.
  • Intramolecular Geometry
    • Bonds
    • Angles
    • Torsions (Newman Projections)
    • Least squares planes
    • Rings (Cremer & Pople analysis)
  • Inter-molecular contacts
    • Hydrogen-Bond analysis
    • Ring-Ring interactions
  • Coordination Geometry
    • Berry Pseudo-rotation (TBP-SP)
  • MolFit

• Descriptors
  • R/S-determination
  • Puckering descriptors
  • Coordination descriptors

• Tests
  • ADDSYM (building on Yvon LePage's powerful published MISSYM (C) algorithm)
  • VOIDS
  • TLS-Rigid group analysis
  • Hirshfeld Rigid Bond
  • TwinRotMat: Check for (analysis of) unresolved twinning based on '.fcf' data.

• Utilities
  • Cell transformation
  • SHELXL input etc.), PDB & CIF output
  • Pathway to the CSD to search related structures.

• Graphics
  • Automatic labelled 'ORTEP-lookalike plots
  • The molecular graphics program PLUTON
  • NEWMAN plots
  • Contoured Fourier maps
  • Inspection for completeness of the dataset with ASYM-VIEW

• Several filters
  • Exact (analytical/ de Meulenaer & Tompa) face-indexed correction for absorption
  • DELABS (the locally modified Walker & Stuart DIFABS technique for empirical absorption correction)
  • Psi-scan based correction for absorption
  • Correction with MULABS using multiple scanned reflections following the Blessing algorithm
  • SQUEEZE for handling disordered solvents (= BYPASS procedure, (v.d. Sluis & Spek, Acta Cryst. (1990), A46, 194)).

• Validation
  • Validation checks for data supplied in CIF-Format, implementing most published tests done in Chester on papers submitted for publication in Acta Cryst + a large number of 'PLATON-related' tests.

• Publication
  • Supplementary Material
  • CIF-generation for Acta Cryst C

• Interfaces to other Packages
  • POVRAY
  • RASMOL
  • RASTER3D
  • CSD-QUEST
  • F3D

• The SYSTEM-S Interface

• Data reduction of CAD4 data (program HELENA)

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

• CIF - The standard Crystallographic Interchange Format (s810c.cif)
• FDAT - The Cambridge Crystallographic database Format (azt.dat)
• PDB - A rather loose format in use in the modelling and protein world. (ml.pdb)
• RES - SHELX standard (No esd's) (s913a.res)
• SPF - A rather flexable local format ideal for manual free format (cyto.spf)
• CART3D - Angstrom Coordinate Format input specification. (c540.cart3d)

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

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

A similar filter may be setup to do a DIFABS-type of absorption correction.

>> CALC DELABS

This should be done in a separate platon run. You will need a 'shelxl.ins' and a 'shelxl.hkl' (TYPE 4 - with direction cosines on it in the SHELX-76 style - their validity is checked. The program HELENA - also on this ftp - generates the required file for CAD4 diffractometer output) 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 with) cell transformation matrices, scaling factors, anisotropic displacement parameter model etc.

See also the Web-Pages:

PLATON/ABSCOR-Manual (Absorption Correction)

PLATON-Manual

PLUTON-Manual

PLUTON

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

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

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

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

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

RASMOL

• CAVEAT: This is a RESEARCH-program that is upgraded regularly on an event-driven basis related to the needs (experience, bug reports, new insight) of our national single crystal service facility (over 200 mainly organometallic structures/year), local crystallographic research, CIF's received as coeditor of Acta Cryst C and external user reports. It represents the current status (with possible loose ends to be filled in later or options needing fine-tuning in the field).

• Extensive local modification of the source code is discouraged. There are usualy major changes in the source code between released versions. (For this reason, most comment is left out from the distributed source code).

• Please inform me about problems and check regularly for more up-to-date versions (where problems encountered may have been solved in the meantime). Please sent the insulting files to 'a.l.spek@chem.uu.nl'.

• THANKS: to all users who contribute(d) in many ways to the development of the features now present in PLATON and authors of crystallographic software who may find some of their excellent ideas intertwined into PLATON.

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@chem.uu.nl
WWW : http://www.cryst.chem.uu.nl/
WWW : http://www.cryst.chem.uu.nl/platon/

PLATON HOMEPAGE