WHAT IS PLATON AND HOW TO GET STARTED
PLATON (C) 1980-2020 A.L.Spek, Utrecht University, Padualaan 8, 3584 CH,
Utrecht, The Netherlands.
WHAT IS PLATON ?
is a versatile
compatible multipurpose crystallographic tool.
Most PLATON features complement those available in the excellent
and widely distributed SHELX2018 and later 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.
- PLATON. The molecular geometry tool.
This is the (generic) native mode when the executable is invoked as platon
- PLUTON. The molecular graphics tool.
This mode is entered, as opposed to through a platon instruction option,
when invoked (via a softlink to platon i.e. 'ln -s platon pluton')
as pluton or (with the command line option '-p') as platon -p
- SYSTEM S. The crystallographic supervisor shell.
This mode is entered when invoked (via a softlink to platon)
as s or platon -s
Note: This tool is currently not actively maintained.
- CIFCHK. The CIF Validation tool.
This mode is entered when invoked (via a softlink to 'cifchk')
as cifchk or as platon -u
- HELENA. Data reduction (i.e. generation of 'shelx.hkl') from
This mode is entered when invoked as helena or platon -k
- STIDY. Standardisation of inorganic structural parameters
following Parthe & Gelato.
This mode is entered when invoked as stidy or platon -Y.
WHAT DOES PLATON OFFER
PLATON implements the following features:
- A large variety of standard geometrical calculations, either fully automatic or as specified in detail.
- Intramolecular Geometry
- 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)
- Puckering descriptors
- Coordination descriptors
- ADDSYM (building on Yvon LePage's powerful published
MISSYM (C) algorithm)
- TLS-Rigid group analysis
- Hirshfeld Rigid Bond
- TwinRotMat: Check for (analysis of) unresolved twinning based on
- Cell transformation
- SHELXL input etc.), PDB & CIF output
- Pathway to the CSD to search related structures.
- 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
- Correction with MULABS using multiple scanned reflections following the
- SQUEEZE for handling disordered solvents
(= BYPASS procedure, (v.d. Sluis & Spek, Acta Cryst. (1990), A46, 194)).
- 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.
- Supplementary Material
- CIF-generation for Acta Cryst C
- Interfaces to other Packages
- The SYSTEM-S Interface
- Data reduction of CAD4 data (program HELENA)
Note: Most PLATON features are currently available only for non-protein
Depending on the desired type of calculations PLATON requires, similar to SHELX97,
two ASCII files (vide infra):
- a coordinate (instruction) file (CIF,PDB,RES.FDAT,SPF)
- 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
- CIF - The standard Crystallographic Interchange Format
- FDAT - The Cambridge Crystallographic database Format
- PDB - A rather loose format in use in the modelling and protein world.
- RES - SHELX standard (No esd's)
- SPF - A rather flexable local format ideal for manual free format
- CART3D - Angstrom Coordinate Format input specification.
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 and later style FO/FC CIF's as
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
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 >>):
(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),
>> 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)
RECIPROCAL LATTICE SYMMETRY
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
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
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
RAY-TRACED AND RASTER MOLECULAR GRAPHICS
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.
Rendered ORTEP presentations may obtained through PLATON using
Note: a tiff-file is produced. An attempt is made to display this
file either with xv, gimp or display software.
Access to RASMOL through PLATON/PLUTON is available by implementing
- 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
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
3584 CH Utrecht
WWW : http://www.platonsoft.nl/
WWW : http://www.platonsoft.nl/platon/