What is PLATON and ....
What is PLATON and how to get started
Version 2-February-1998
PLATON is a versatile SHELX97 compatible crystallographic tool implementing:
- a large variety of standard geometrical calculations (i.e. bonds, angles,
torsions, planes, rings, inter-molecular contacts (H-Bond analysis),
Coordination etc.),
- tests: (i.e. ADDSYM (building on Yvon LePage's powerful published
MISSYM (C) algorithm), VOIDS etc.),
- utilities: (cell transformation, SHELXL input etc.), PDB and CIF output
- graphics: (e.g. automatic labelled 'ORTEP-lookalike plots, the molecular
graphics program PLUTON and NEWMAN plots)
- several filters: (i.e. Exact (analytical/ de Meulenaer and Tompa)
face-indexed correction for absorption, DELABS (the locally modified
Walker and Stuart
DIFABS technique for empirical absorption correction) and SQUEEZE for
handling disordered solvents (= BYPASS procedure, (v.d. Sluis and Spek,
Acta Cryst. (1990), A46, 194))).
- Validation checks for data supplied in CIF-Format.
Most PLATON features complement those available in the widely distributed
public domain SHELX97 package.
WHAT COORDINATE DATA INPUT STANDARDS ARE ACCEPTED
=================================================
Parameter data may be given in various formats including CSD-FDAT, CIF, PDB and
SHELX-RES standards. 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 DATA FORMAT
======================
Reflection data should be provided in the SHELX format (optionally with
SHELX76-style direction cosines.
WHAT DOES IT COST?
==================
The Program may be used free of charge by the academic community under
the condition that it is not redistributed (just give the pointer to
this anonymous ftp server (xraysoft.chem.ruu.nl) for a current and fresh copy.
The author is interested in reports of misbehaviour and suggestions for
additional features.
There is a charge of US$ 5000 for commercial users (as a contribution
to our continuing research efforts).
HOW TO OBTAIN A COPY OF PLATON
==============================
In order to get a copy of the program source you will have to copy
(and uncompress) the two files platon.f.Z and xdrvr.c and compile
and link them into an executable with the name 'platon' (see example file
with the name compile) and when desirable, a soft link pluton to
platon.
(A compiled version - not always up-to-date - may be extracted by
copying and uncompress platon.Z from the appropriate platform
directory)
Alternatively, copy 'platon.tar.Z' which contains all files
in the generic 'unix' directory (will compile without any change on DEC,
SGI and LINUX platforms).
HOW TO COMPILE
==============
On most UNIX implementations a compile line like the one given below
should be sufficient:
f77 -o platon platon.f xdrvr.c -lX11
Some compilers need additional options (e.g. -Nl250). Some compilations
crash when there is no sufficient space in /tmp. Use a cshell command such as
setenv TMPDIR .
instead (or any other directory with enough scratch space). Some
compilers only function when the source code platon.f has been split
in smaller pieces (try parts of 10000 lines each) to be compiled separately.
MENUS AND MOUSE CLICKING
========================
PLATON (UNIX-version) attempts by default to open an X-Window Menu.
When it doesn't succeed, it automatically switches to interactive input
from the keyboard and TEK4010 graphics (Keyboard input as default is
choosen when PLATON is called with the '-o' option.)
In the menu mode, input can be given either from the keyboard (useful
for the more complex instructions) or via mouse clicks.
The X-window is devided in four sub-windows.
1 - The main graphics area in the upper-left one (also used for the main
PLATON menu).
2 - The upper-right window carries varies sup-menus with clickable options.
Currently active options are displayed in RED.
3 - The Lower-Left window is used for short messages and the display of
keyboard input
4 - The lower-right window informs about the current input status.
INTRODUCTORY 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 (excluding quotes):
'platon sucrose'
followed by the interactive instructions (on the program prompt >>):
>> CALC
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.
ANALYTICAL ABSORPTION CORRECTION
================================
For those having crystals that can be face-indexed there is the
easy-to-use implementation of the de Meulenaar and Tompa absorption
correction method.
This filter may be invoked with:
platon shelxl.ins
again, you will need a 'shelxl.hkl' file including the direction cosines
The file shelxl.ins 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 and mu should be given either both in
mm or both in cm.
See also the Test-example directory.
RECIPROCAL LATTICE SYMMETRY
=========================
The symmetry of the reciprocal lattice at hand may be inspected with
the PLATON/ASYM utility for a given shelx.hkl file. See test directory.
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 and 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).
X-WINDOW MENU
=============
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 or by starting the program with the '-o' option
on the command line.
PLUTON: (via platon -p or pluton --> platon soft link)
======
By default, a PLOT instruction will bring up a MENU (X-window mode only)
from which mouse-driven options may be run. The more complex
instructions may be given via the keyboard. The menu-feature is switched
off either through a menu option or with the instruction MENU OFF
(to be given before the first PLOT instruction).
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)).
RAY-TRACED 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.
PRINTING
========
PLATON generates an extensive listing file '?.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.
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.
One of the options to run the feature on 'sk5555.cif' is via:
platon -u sk5555.cif
The check-output can be found in: sk5555.chk
Note: make sure that the file 'check.def' is present in the current
directory
Alternatively, the feature can be run from the platon opening window.
Note: This validation procedure is intended as a 'structural' addition
to the checking already done by the Chester Acta Cryst office
for 'C-papers'. It does not support all the published checks
done in Chester.
MISCELLANIOUS
=============
Further information on available instructions is obtained with
the instruction:
HELP
**********************
Caveat: This is a RESEARCH-program that is upgraded regularly on an
event-driven basis on 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
'spea@chem.ruu.nl'.
Note: A manual (not up to date, but adequate to pick up the general
procedure) is available in the unix/platon sub-directory
A manual in HTML format is in preparation.
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 will find some of their
excellent ideas intertwined into PLATON.
----------------------
Dr. A.L. Spek
Bijvoet Centre for Biomolecular Research
Vakgroep Kristal and Structuurchemie,
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands.
Email: spea@chem.ruu.nl
WWW : http://www.cryst.chem.ruu.nl/sonuu.html
Pairwise Molecule FITTING
=========================
PLATON contains a FIT routine based on quaternion rotation (A.L. Mackay,
Acta Cryst. (1984), A40, 165-166).
The general instruction to fit two molecules or residues is:
FIT At11 At21 At12 At22 .....(etc)
where atoms to be fitted are given pairwise.
Note: The FIT instruction may be broken up over more than one line.
Lines that are to be continued should end with '='.
There are two modes of operation:
1 - when specified before any CALC instruction, the actual calculation
will be done along with the subsequent CALC GEOM or CALC INTRA
calculation. Listing of the results will be on the '.lis' file
only.
2 - when specified after a CALC INTRA or CALC GEOM calculations will
be done directly. Listing of the results of the calculation are both
on the interactive output window and in the listing file.
A special case is the situation where the two molecules to be fitted
have similar numbering of the atoms. The automatic sorting feature of
PLATON will put the atoms in the same order. In such a case,
specification of only one atom from each of the molecules will be
sufficient to fit all non-hydrogen atoms in both molecules
e.g.
FIT O11 O21
SQUEEZE, An effective cure for the disordered solvent syndrome in
crystal structure refinement.
==================================================================
See Abstract M05 (page 66) ACA-94 Atlanta/USA.
The current version has been designed, dimensioned and tested for small
moiety structures containing disordered molecules of the type toluene, CH2Cl2,
tetrahydrofurane etc..
Large voids currently require significant computing in the stage where the
size and shape of the solvent accessible void is determined.
Reflection data and FFT-array are stored in memory i.e. large structures
may require large amounts of memory (change parameter NP21 globally to a
larger value).
SQUEEZE has been implemented as the 'SQUEEZE option' in the program
PLATON.
PLATON/SQUEEZE should be compatible with small-moiety structure
refinement usage of the program SHELXL-93.
The program is used as a filter. Input files are
- shelxl.hkl - (HKLF type 4)
- shelxl.res - (complete set of refined model parameters, including
hydrogen atoms but excluding any dummy atoms used to
describe the disorder region)
invoke the program with:
platon shelxl.res
give on the prompt >> the instruction:
CALC SQUEEZE
The result will be:
- shelxl.lis: a listing file giving details of the calculations
- shelxl.hkp: a modified reflection file against which the ordered
structure parameters can be refined (the solvent
contribution has been eliminated from the reflection
data.)
In order to run SHELXL-93 on the 'solvent-free' Fo^2 data:
(Note: save all files you want to keep)
- cp shelxl.res shelxl.ins
- cp shelxl.hkp shelxl.hkl
- run shelxl
In order to get an .fcf style file (Fo^2 + Fc^2 (model + solvent))
you will need shelxl.hkl (= shelxl.hkp) and shelxl.res
run: platon shelxl.res
with the interactive option: CALC FCF
The procedure (starting from the original reflection data) can be
repeated using the newly refined parameters when desired.
The general procedure has been described in more detail in:
Acta Cryst. (1990), A46, 194 as the 'BYPASS procedure' P. v.d. Sluis
and A.L. Spek)
The 'difference-map' improvement potential of this technique is
demonstrated for small molecule structures. The technique should also
work for protein data. However, this has not been tested by us as yet with
PLATON/SQUEEZE. Current design features may cause problems when tried.
A directory containing a test-example is in dec5000/platon/SQUEEZE_TEST.
Notes:
======
- The record length of the '.hkp' file has been increased above 80
to accomodate additional data (the exact details are not fixed)
- The SHELXL-TWIN instruction is not available as yet in PLATON.
- Current conditions for applicability are:
1 - Reasonable data-resolution (say 25 degrees Mo)
2 - Structure of the known part completed with H-atoms
3 - No more than 26 'voids' in the unit-cell
4 - Disorder density should be well outside the vanderWaals
service of the known structure.
5 - The area to be 'SQUEEZE' should not be too large (say
less than in the order of 30% of the unit-cell volume.