PLATON is a versatile SHELX97 compatible crystallographic tool implementing:
Most PLATON features complement those available in the widely distributed public domain SHELX97 package.
Note: Most features are currently available only for non-protein structures.
Depending on the desired type of calculations PLATON requires, similar to SHELX97, two ASCII files: a coordinate (instruction) file and optionally a reflection file.
Parameter data may be given in various formats including CSD-FDAT, CIF,
PDB & 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 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.
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.uu.nl) for a current & 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).
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).
For the Validation feature, a copy of the file 'check.def' will be needed along with a copy of VALIDATION.DOC for an explanation of each test.
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.
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 as detailed in the PLATON MANUAL or PLUTON MANUAL) or via mouse clicks.
The X-Window area is devided in four sub-windows.
Left-button clicks with the mouse on menu items invoke calculations.
Right-button clicks on menu items generate a help/info page.
More extensive output is produced on the window from which the program was started and on the listing file (.lis).
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
(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:
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 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 & mu should be given either both in mm or both in cm.
See also the Test-example directory.
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.
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.
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).
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.
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 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)).
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.
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, set the environment variable CHECKDEF to where this
file is located.
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.
Further information on available instructions is obtained with the instruction:
HELP
Dr. A.L. Spek
Bijvoet Centre for Biomolecular Research
Vakgroep Kristal & Structuurchemie,
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands.
Email: spea@chem.uu.nl
WWW : http://www.cryst.chem.uu.nl/
WWW : http://www.cryst.chem.uu.nl/platon/