Most PLATON features complement those available in the excellent and widely distributed 'public domain' 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 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 structure determination process in a UNIX environment)
Currently, SYSTEM-S constitutes one of the build-in pathways through PLATON.
This is the (generic) native mode when the executable is invoked as platon
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
This mode is entered when invoked (via a softlink to platon) as s or platon -s
This mode is entered when invoked (via a softlink to 'cifchk') as cifchk or as platon -u
This mode is entered when invoked as helena or platon -k
Note: introduce link ln -s platon pluton for direct access to PLUTON etc.
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):
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)
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 >>):
(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)
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.
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
Postscript files can be printed on non-postscript printers with the programs ghostscript and ghostview, available from http://www.cs.wisc.edu/~ghost
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.
Note: a tiff-file is produced. An attempt is made to display this file either with xv, gimp or display software.
Dr. A.L. Spek
Bijvoet Centre for Biomolecular Research
Vakgroep Kristal & Structuurchemie
3584 CH Utrecht
The Netherlands. Email: email@example.com
WWW : http://www.cryst.chem.uu.nl/
WWW : http://www.cryst.chem.uu.nl/platon/