Example: setenv CHECKDEF /mnt/user/check.def
The results of the validation can be found on the file '
.chk'
The preparation of a small shell script may be helpful. Below is an example of such a script
that can be made available systemwide by placing it in /usr/local/bin
#!/bin/csh
ln -sf /mnt/spea/acc/check.def
platon -u $1.cif
/usr/sbin/unlink check.def
less $1.chk
The validation than runs for CIF sk1000.cif by:
chk sk1000
Example of a Validation Report
#===============================================================================
# PLATON/CHECK run versus check.def version of 08/02/00 for entry: I
# Data From: e60.cif - Data Type: CIF
# CELL 1.54178 16.645 25.768 7.066 90.00 90.00 90.00 3030.70
# SpaceGroup P212121 Rep: P 21 21 21
# MoietyFormula C34 H52 O4
# Reported C34 H52 O4
# SumFormula C34 H52 O4 Rep: C34 H52 O4
# Mr = 524.76[Calc], 524.76[Rep]
# Dx,gcm-3 = 1.150[Calc], 1.150[Rep]
# Z = 4[Calc], 4[Rep]
# Mu (mm-1) = 0.568[Calc], 0.568[Rep]
# Reported T limits: Tmin=0.940 Tmax=0.970 '\Y SCAN'
# Calculated T limits: Tmin=0.815 Tmin'=0.797 Tmax=0.945
# Reported Hmax= 20, Kmax= 31, Lmax= 8, Nref= 3292 , Th(max)= 70.01
# Calculated Hmax= 20, Kmax= 31, Lmax= 8, Nref= 3291( 5758), Ratio= 1.00( 0.57)
# R= 0.0463( 2929), wR2= 0.1367( 3292), S = 1.162, Npar= 347, Flack=-0.40( 4)
#===============================================================================
>>> The Following ALERTS were generated <<<
052_ALERT A (proper) absorption correction method missing
702_ALERT A Rep. Angle 174 Dev. from Calcd 110.00 5.00 Sigma
702_ALERT A Rep. Angle 176 Dev. from Calcd 110.00 5.00 Sigma
702_ALERT A Rep. Angle 177 Dev. from Calcd 109.00 5.00 Sigma
702_ALERT A Rep. Angle 183 Dev. from Calcd 109.00 5.00 Sigma
#===============================================================================
222_ALERT B Large Non-Solvent H Ueq(max)/Ueq(min) . 4.02 range
#===============================================================================
032_ALERT C Std Uncertainty in Flack parameter too high .. 0.40
033_ALERT C Flack Parameter value deviates from zero ..... -0.40
057_ALERT C Correction for absorption required RT(exp) = 1.16
089_ALERT C Poor Data / Parameter ratio .................. 9.49
220_ALERT C Large Non-Solvent C Ueq(max)/Ueq(min) . 3.23 range
412_ALERT C Short intra XH3 .. XHn : H(242) .. H(253) = 1.81 Ang.
412_ALERT C Short intra XH3 .. XHn : H(251) .. H(262) = 1.83 Ang.
701_ALERT C Rep. Bond 61 Dev. from Calcd 0.9614 1.43 Sigma
701_ALERT C Rep. Bond 81 Dev. from Calcd 0.9588 1.23 Sigma
702_ALERT C Rep. Angle 167 Dev. from Calcd 109.40 1.03 Sigma
Chapter 9 - Ab-initio Structure Solution by Charge Flipping
The FLIPPER option in PLATON implements the Charge Flipping algorithm for
ab-initio
structure determination. This method was first introduced by Oszlanyi & Suto (2004, 2005)
as an alternative structure determination procedure for high resolution (small molecule)
structures. The required input consists of a SHELX style input file (
name.ins) and a
reflection file (
name.hkl). Alternatively, a
name.cif and a
name.fcf can be supplied to test
the potential of the program with a known structure. The data is the .
hkl or .
fcf are
expanded to P1 on the basis of the Laue group of the structure that is derived from the
symmetry information in the .
ins or .
cif). The program is started via the command line
instruction
platon name.ins or
platon name.cif.
A default Charge Flipping run (with 25 random phase starting points) is invoked by clicking
on the
FLIPPER entry on the main PLATON menu. The same operation is invoked directly
from the command line with the instruction
platon -Z name.ins or
platon -Z name.cif.
I
n
the default mode, a sequence a random starting phase sets will be optimized until a stable
solution is found with an R-value below 30 percent. The resulting peak list (on the file
name_flp.res) is subsequently optimized (on file
name_xor.res) with
PLATON/EXOR
and investigated for the correct space group (result in
name_sol.res). The best solution
name_res.res is displayed with the PLUTON link in PLATON (allowing for the deletion
and/or renaming of atoms and thus producing a starting file for refinement with SHELXL on
name_res.new).
Alternatively, Charge Flipping is invoked with the keyboard instruction:
FLIP ntry nloop nsolve delta perc Uiso
where:
ntry is the number of trial random phase starts (default = 25).
nloop is the maximum number of flip cycles (default = 250,500,1000,2000).
nsolve is the number of attempted solutions before termination (default = 3)
delta is the fraction of the maximum density in the map below which the sign of the density
is flipped (default = 0.02).
perc Percentage of reflections treated as weak for which the calculated phase is shifted by
90 degrees. (default = 25)
Uiso is the value used in the expression exp(Uiso*8*pi**2*(sintheta/lambda)**2) as a
multiplication factor for F(obs) (default = 0.02).
Example of a non-default keyboard instruction:
FLIP 10 50 3 0.02 5 0.02.
Example of a
name.ins file:
TITL test
CELL 0.71073 10 11 12 80 90 100
ZERR 1 0.0001 0.001 0.001 0.01 0.01 0.01
SPGR P21/c
SFAC C H O
UNIT 20 24 12
HKLF 4
As test files download
flip.ins
and
flip.hkl
or
vitac.cif
and
vitac.fcf
Notes: