Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht

9.3 PLATON - ANALYSE Menu

 

WinGX v1.64

Chapter. 9.3  PLATON

30

8. Atomic radii used in PLATON

 Ac  1.88        Er  1.73        Na  0.97        Sb  1.46

 Ag  1.59        Eu  1.99        Nb  1.48        Sc  1.44

 Al  1.35        F   0.64        Nd  1.81        Se  1.22

 Am  1.51        Fe  1.34        Ni  1.50        Si  1.20

 As  1.21        Ga  1.22        Np  1.55        Sm  1.80

 Au  1.50        Gd  1.79        O   0.68        Sn  1.46

 B   0.83        Ge  1.17        Os  1.37        Sr  1.12

 Ba  1.34        H   0.23        P   1.05        Ta  1.43

 Be  0.35        Hf  1.57        Pa  1.61        Tb  1.76

 Bi  1.54        Hg  1.70        Pb  1.54        Tc  1.35

 Br  1.21        Ho  1.74        Pd  1.50        Te  1.47

 C   0.68        I   1.40        Pm  1.80        Th  1.79

 Ca  0.99        In  1.63        Po  1.68        Ti  1.47

 Cd  1.69        Ir  1.32        Pr  1.82        Tl  1.55

 Ce  1.83        K   1.33        Pt  1.50        Tm  1.72

 Cl  0.99        La  1.87        Pu  1.53        U   1.58

 Co  1.33        Li  0.68        Ra  1.90        V   1.33

 Cr  1.35        Lu  1.72        Rr  1.47        W   1.37

 Cs  1.67        Mg  1.10        Re  1.35        Y   1.78

 Cu  1.52        Mn  1.35        Rh  1.45        Yb  1.94

 D   0.23        Mo  1.47        Ru  1.40        Zn  1.45

 Dy  1.75        N   0.68        S   1.02        Zr  1.56

Note: OW is equivalent to O and Q1 is equivalent to C1.

Covalent radii are those given in the Cambridge Structural data base manual.

9.  Internal parameters

The program contains internal integer and real parameter arrays (IPR and PAR respectively).

They include default parameter settings and values that may be either explicitly or implicitly

manipulated with the (sub)keywords. Below is a list of some of them. Their values may be

changed with SET PAR and SET IPR instructions or examined with LIST PAR and LIST IPR

instructions. It should be noted that there is no checking for side-effects.

IPR(141) - Nplane parameter in TME

IPR(142) - Lines  parameter in TME

PAR(73)  - Letter size

10. CIF-validation documentation (VALIDATION.DOC)

This document should provide information on the CIF-validation tests as

specified in the file 'check.def' and implemented in PLATON.

# check.def contains the tests, error thresholds and warning messages

#    issued by the program PLATON when run in the 'VALIDATION' mode

#

#           This file is read when PLATON is called with the '-u' switch

#                    (e.g. 'platon -u sk1500.cif')

#

# - Test output will be in the order as defined implicitly below

#

---

9.3 PLATON - ANALYSE Menu

 

WinGX v1.64

Chapter. 9.3  PLATON

31

# - Tests are identified with three-digit numbers

#   _0xx - general

#   _1xx - cell/symmetry

#   _2xx - adp-related

#   _3xx - intra geometry

#   _4xx - inter geometry

#   _5xx - coordination geometry

#   _6xx - void tests

#   _7xx – various test

#

_000-_013 : Pseudo Requests

This set of pseudo requests generates a listing of some relevant reported

and calculated data including transmission range and completeness of the

data set.

_020 : Check on R(int)

R(int) should be well below 10% and in the order of magnitude of the

reported R-values. R(int) may be relatively meaningless when based on a

very limited number of averaged data.

_021 : Check ratio of observed/expected number of reflections 

The expected number of reflections corresponds to that in the asymmmetric

unit of the Laue group.

Expected ratio:  less-or-equal 1 for centro symmetric structures and 

less than 2 for non-centrosymmetric structures. 

Reasons to exceed those numbers can be:

1 - Systematic extinction not omitted from the observed data count

2 - Refinement with redundant (i.e. not averaged/unique) data set.

_022 : Check for completeness 

Test for data completeness. The ratio of the reported number of unique

reflections and expected for the resolution given.

_023 : Check Theta-max 

Check resolution of the data set. Alerts are issued when sin(theta)/lambda

< 0.6

_024 : Check for Friedel Averaging Preferred

Averaging of Friedel pairs is preferred for MoKa datasets containing atoms

not heavier than Si. Use MERG 4 for SHELXL97 refinements.

_025 : Check h,k,l - range 

Check reported h,k,l - range with calculated range based on reported theta-

max.

_026 : Check for weak data

---

9.3 PLATON - ANALYSE Menu

 

WinGX v1.64

Chapter. 9.3  PLATON

32

Check whether a sufficient fraction of the unique data is indeed above the

2 sigma level.

_030 Check on meaningfully refined extinction parameter.

This test checks whether a refined extinction parameter is meaningful i.e.

whether its value is significantly larger than its corresponding s.u. If

not, this parameter should be removed from the model and the structure

refined without this meaningless additional  parameter. The current default

gives a warning when it value is within 3.33 s.u.

_032 Check S.U. of the Flack parameter

Check meaningfulness of Flack parameter 

_033 Check deviation of Flack parameter from zero 

Check validity of absolute stucture determination 

_040 Check for the presence of H-atoms in carbon containing compounds.

Alert for 'no H-atoms' in CIF

_041 Compare the Reported and Calculated Sum Formula

_042 Compare the reported and Calculated Moiety Formula

_043 Compare Reported and Calculated  Molecular Weight

Note: atomic weights used in the calculation of the molecular weight are

those used in SHELXL97.

_044 Compare Reported and Calculated density

_045 Compare Reported and Calculated Z

_046 Check on Reported Z, MW, D(calc) consistency

D(calc) as calculated from the reported Z and MW is compared for

consistency with the reported d(calc).

_050 Test for mu given

_051 Test diference of reported and calculated mu

_052 Test for specification of absorption correction method

---