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Re: CoreCIF revision 2.3
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Re: CoreCIF revision 2.3
- From: Brian McMahon <bm@iucr.org>
- Date: Thu, 26 Jun 2003 16:03:52 +0100 (BST)
Dear David
I am slightly leapfrogging your considered tidying up of the suggested
core enhancements by reviewing and commenting on some items that have
previously passed in front of the group. The most substantial comments are
some way down, referring back to the recent list #6.
First, though, I have a few editorial comments on the items approved from
lists 1 through 5.
----------------------------------------------------------------
_chemical_properties_biological
_chemical_properties_physical
Both data names (and their data block codes) were mis-spelled as
_chemcial_. Since these were both requested by CCDC I wonder whether our
friends there can find us some suitable examples from the CSD?
----------------------------------------------------------------
_diffrn_source_take-off_angle
The definition seems a little sparse, but might be adequate. I wondered
whether it should say "The angle between the normal to the surface of the
target and the X-ray beam..."? This still assumes that the area of the
target illuminated by the X-ray beam is perfectly flat. If not, should it
say further "... and the midline of the X-ray beam..."? Pedantic, perhaps,
but it's better to be explicit.
----------------------------------------------------------------
_diffrn_reflns_measured_fraction_resolution_full
_diffrn_reflns_measured_fraction_resolution_max
_diffrn_reflns_resolution_full
_diffrn_reflns_resolution_max
(1) Typo in _fraction_ ("_faction_") x 2
(2) I wonder whether these should properly have
"_related_function replace" since they're not strictly replacements
(i.e. they describe different quantities). "alternate" may be better,
as in the relationship between U and B temperature parameters. I read
"alternate" as saying "You wanted such-and-such a quantity; it's not
present, but if you're interested, the similar so-and-so might be of
interest". Perhaps Syd can help us here. (If we can't resolve this, it
would be OK to drop the _related_ items altogether.)
----------------------------------------------------------------
SPACE_GROUP and SPACE_GROUP_SYMOP items
Assuming that you include in the core dictionary only those items put
forward in the proposal, then the following things need attention:
_type in the categories should be 'null' (not 'nul')
The category example for SPACE_GROUP needs to omit the following lines:
_space_group_name_Schoenflies C2h.6
_space_group_Bravais_type mS
_space_group_Laue_class 2/m
_space_group_centring_type C
_space_group_Patterson_name_H-M 'C 2/m'
The entry _space_group_name_H-M 'C 2/c'
in this example block is wrong - should be _space_group_name_H-M_alt
In _space_group_name_H-M_alt you need to omit the reference to
_space_group_name_H-M_alt_description in the definition and omit the
use of _*_description in the example loop.
In the category example for SPACE_GROUP_SYMOP, omit
_space_group_symop_operation_description
For _space_group_symop_operation_description omit the 'alternate' relation
citing _space_group_symop_generator_xyz
Omit '_space_group_Wyckoff_sg_id' as a _list_link_child of _space_group_id
In _space_group_symop_sg_id the references to _space_group.id should be
replaced with the DDL1 equivalent.
I wonder whether _space_group_id (and its remaining child
_space_group_symop_sg_id) are needed at all in this core version. If it is
supposed that the DDL1 version is used only for reporting a space group
assigned to a structure (which seems to be implied by the items from the
full dictionary that you have selected), will there ever be cases when
you need to loop data items in the SPACE_GROUP category?
On the other hand, the insertion of a formal category key for each new
category introduced may make it easier to carry this onwards to
applications such as mmCIF that do use DDL2. I don't feel strongly about
this.
----------------------------------------------------------------
_exptl_crystal_colour_ items
Delete the _enumeration_detail column altogether - the enumeration values
are self-explanatory.
==============================================================================
COMMENTS ON #6
--------------
ATOM_TYPE_SCAT category
I don't have any quibble with the individual definitions that David has
proposed, but I am concerned about the name collision with existing
_atom_type_scat_* items that so far have been looped with other
_atom_type_ data names, e.g.
loop_
_atom_type_symbol
_atom_type_oxidation_number
_atom_type_number_in_cell
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B
H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B
O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B
N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B
If the scattering factors are dependent on wavelength and scattering
angle, what exactly do the numbers in the above example refer to anyway?
Is it the case that items like the Cromer-Mann coefficicients (which, as I
understand it, are used in an analytic approximation to scattering factors
in a function of lambda and theta) could remain in the old category, and
the lambda or theta-dependent items that have been introduced comprise the
proposed new category? A more distinctive name for such a new category would
be ATOM_TYPE_SCATTER; the distinction between ATOM_TYPE_SCAT and
ATOM_TYPE_SCATT would be lost to the average user).
REFINE category
When I read through the proposal, it seemed to me eminently sensible.
However, when I scanned through a few hundred CIFs in our production
directories, I found the situation in practice to be less clear. In the
sample of files I tested are found the following distinct entries for
_refine_ls_extinction_method:
none
'B-C type 1 Gaussian isotropic (Becker & Coppens, 1974)'
'B-C type 1 Lorentzian isotropic (Becker & Coppens, 1974)'
'Larson (1970)'
'Larson 1970 Crystallographic Computing eq 22'
'shelxl'
SHELXL
'SHELXL 97'
'SHELXL96 (Sheldrick, 1996)'
SHELXL97
'SHELXL97 (Sheldrick, 1997)'
'SHELXL97 in SHELXTL (Sheldrick, 1997)'
SHELXTL
'SHELXTL (Bruker, 1997)'
'SHELXTL (Bruker, 1998)'
'SHELXTL (Sheldrick, 1997)'
'SHELXTL (Sheldrick, 2001)'
SHELXTL97
'Zachariasen (1967)'
'Zachariasen (1967) type 2 Gaussian isotropic'
'Zachariasen_type_2_Gaussian_isotropic (Zachariasen, 1967)'
'secondary Zachariasen'
Zachariasen
Zachariasen_type_2_Gaussian_isotropic
'F*=F(1+0.002xF^2^(sin(2\q))^-0.25^'
(The last of course really should be in _refine_ls_extinction_expression)
There are also surprisingly few distinct expressions given; the ones I
have found are
'Eq22 p292 "Cryst. Comp." Munksgaard 1970'
'Eq22 p292 Cryst. Comp. Munksgaard 1970'
Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
'FC^*^=KFC[1+0.001XFC^2^\L^3^/SIN(2\Q)]^-1/4^'
'Fc^*^ = kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^'
'Fc^*^=3DkFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^'
'Fc^*^=KFc[1+0.001xFc^2^\1^3^/sin(2\q)]^-1/4^'
'Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^'
'Fc^*^=kFc[1+0.001xFc^2^l^3^/sin(2q)]^-1/4^'
'F~c~^*^ = kF~c~[1+0.001xF~c~^2^\l^3^/sin(2\q)]^-1/4^'
Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
'equation (22) of Larson (1970)'
?
none
not_defined
not_refined
These appear all to be attempts to express equation 22 of the cited
reference, which in TeX is
$$ F^*_c = k |F_c| (1 + 2 r^* |F_c|^2\delta) ^{-1/4} $$
and is presumably what is meant by the "Zachariasen" method. According to
the existing core definition, _refine_ls_extinction_coef should supply the
r* value in this case, the magnitude of which should be ~10000.
The values of _refine_ls_extinction_coef in our collection of CIFs are
given below. One would of course expect a range of numeric values, since
r* is related to the mean path length through a domain in the crystal and
the mosaic spread; but the vast majority of reported values are 8 or more
orders of magnitude lower than the suggested range, so clearly something
is wrong.
_refine_ls_extinction_coef '8.3(5) \\times 10^-5^'
_refine_ls_extinction_coef 'Not refined'
_refine_ls_extinction_coef 'not applicable'
_refine_ls_extinction_coef 'x = 0.0007'
_refine_ls_extinction_coef .
_refine_ls_extinction_coef 0
_refine_ls_extinction_coef 0.0
_refine_ls_extinction_coef 0.0000
_refine_ls_extinction_coef 0.0000(2)
_refine_ls_extinction_coef 0.00000
_refine_ls_extinction_coef 0.00000(1)
_refine_ls_extinction_coef 0.000000(10)
_refine_ls_extinction_coef 0.00000056
_refine_ls_extinction_coef 0.000098(19)
_refine_ls_extinction_coef 0.000148(2)
_refine_ls_extinction_coef 0.00018(4)
_refine_ls_extinction_coef 0.000227(7)
_refine_ls_extinction_coef 0.00024(2)
_refine_ls_extinction_coef 0.00028(5)
_refine_ls_extinction_coef 0.00029(4)
_refine_ls_extinction_coef 0.00029(7)
_refine_ls_extinction_coef 0.00038(4)
_refine_ls_extinction_coef 0.000397(11)
_refine_ls_extinction_coef 0.00043(17)
_refine_ls_extinction_coef 0.00043(3)
_refine_ls_extinction_coef 0.00045(16)
_refine_ls_extinction_coef 0.00049(11)
_refine_ls_extinction_coef 0.00049(6)
_refine_ls_extinction_coef 0.0005(2)
_refine_ls_extinction_coef 0.00050(8)
_refine_ls_extinction_coef 0.00059(6)
_refine_ls_extinction_coef 0.00064(15)
_refine_ls_extinction_coef 0.00085(8)
_refine_ls_extinction_coef 0.0009(2)
_refine_ls_extinction_coef 0.0009(6)
_refine_ls_extinction_coef 0.00103(6)
_refine_ls_extinction_coef 0.00108(13)
_refine_ls_extinction_coef 0.0011(1)
_refine_ls_extinction_coef 0.00110(10)
_refine_ls_extinction_coef 0.00110(6)
_refine_ls_extinction_coef 0.00113(16)
_refine_ls_extinction_coef 0.0012(5)
_refine_ls_extinction_coef 0.00124(11)
_refine_ls_extinction_coef 0.00125(11)
_refine_ls_extinction_coef 0.00126(7)
_refine_ls_extinction_coef 0.00133(8)
_refine_ls_extinction_coef 0.00136(19)
_refine_ls_extinction_coef 0.00146(18)
_refine_ls_extinction_coef 0.00147(19)
_refine_ls_extinction_coef 0.00149(10)
_refine_ls_extinction_coef 0.0016(3)
_refine_ls_extinction_coef 0.00168(6)
_refine_ls_extinction_coef 0.0017(3)
_refine_ls_extinction_coef 0.0017(4)
_refine_ls_extinction_coef 0.00173(19)
_refine_ls_extinction_coef 0.00179(16)
_refine_ls_extinction_coef 0.0018(2)
_refine_ls_extinction_coef 0.0019(5)
_refine_ls_extinction_coef 0.00190(9)
_refine_ls_extinction_coef 0.00191(12)
_refine_ls_extinction_coef 0.0020(4)
_refine_ls_extinction_coef 0.0022(3)
_refine_ls_extinction_coef 0.0022(5)
_refine_ls_extinction_coef 0.0022(8)
_refine_ls_extinction_coef 0.00229(10)
_refine_ls_extinction_coef 0.0023(2)
_refine_ls_extinction_coef 0.0023(3)
_refine_ls_extinction_coef 0.0023(4)
_refine_ls_extinction_coef 0.0024(2)
_refine_ls_extinction_coef 0.0024(3)
_refine_ls_extinction_coef 0.0024(5)
_refine_ls_extinction_coef 0.00246(15)
_refine_ls_extinction_coef 0.00282(13)
_refine_ls_extinction_coef 0.0029(2)
_refine_ls_extinction_coef 0.0029(9)
_refine_ls_extinction_coef 0.00294(13)
_refine_ls_extinction_coef 0.0030(4)
_refine_ls_extinction_coef 0.0031(5)
_refine_ls_extinction_coef 0.0031(6)
_refine_ls_extinction_coef 0.0032(4)
_refine_ls_extinction_coef 0.0033(9)
_refine_ls_extinction_coef 0.0034(5)
_refine_ls_extinction_coef 0.0035(3)
_refine_ls_extinction_coef 0.0035(6)
_refine_ls_extinction_coef 0.0036(4)
_refine_ls_extinction_coef 0.0036(9)
_refine_ls_extinction_coef 0.004(1)
_refine_ls_extinction_coef 0.0040(4)
_refine_ls_extinction_coef 0.0040(5)
_refine_ls_extinction_coef 0.0041(3)
_refine_ls_extinction_coef 0.0041(7)
_refine_ls_extinction_coef 0.00415(10)
_refine_ls_extinction_coef 0.0043(7)
_refine_ls_extinction_coef 0.0045(11)
_refine_ls_extinction_coef 0.0045(15)
_refine_ls_extinction_coef 0.0045(3)
_refine_ls_extinction_coef 0.0048(6)
_refine_ls_extinction_coef 0.0048(7)
_refine_ls_extinction_coef 0.005(2)
_refine_ls_extinction_coef 0.0050(2)
_refine_ls_extinction_coef 0.0050(7)
_refine_ls_extinction_coef 0.0051(3)
_refine_ls_extinction_coef 0.0053(8)
_refine_ls_extinction_coef 0.0053(9)
_refine_ls_extinction_coef 0.0054(9)
_refine_ls_extinction_coef 0.0055(12)
_refine_ls_extinction_coef 0.0055(8)
_refine_ls_extinction_coef 0.0057(10)
_refine_ls_extinction_coef 0.0058(15)
_refine_ls_extinction_coef 0.0058(45)
_refine_ls_extinction_coef 0.0059(13)
_refine_ls_extinction_coef 0.0061(13)
_refine_ls_extinction_coef 0.0061(17)
_refine_ls_extinction_coef 0.0062(18)
_refine_ls_extinction_coef 0.0062(5)
_refine_ls_extinction_coef 0.0062(6)
_refine_ls_extinction_coef 0.0063(12)
_refine_ls_extinction_coef 0.0064(3)
_refine_ls_extinction_coef 0.0064(6)
_refine_ls_extinction_coef 0.0066(16)
_refine_ls_extinction_coef 0.007(2)
_refine_ls_extinction_coef 0.0072(5)
_refine_ls_extinction_coef 0.0072(8)
_refine_ls_extinction_coef 0.0076(10)
_refine_ls_extinction_coef 0.0076(5)
_refine_ls_extinction_coef 0.0078(11)
_refine_ls_extinction_coef 0.0081(9)
_refine_ls_extinction_coef 0.0083(17)
_refine_ls_extinction_coef 0.0084(18)
_refine_ls_extinction_coef 0.0084(9)
_refine_ls_extinction_coef 0.0086(8)
_refine_ls_extinction_coef 0.009(2)
_refine_ls_extinction_coef 0.0090(4)
_refine_ls_extinction_coef 0.0094(11)
_refine_ls_extinction_coef 0.0095(14)
_refine_ls_extinction_coef 0.0095(9)
_refine_ls_extinction_coef 0.010(2)
_refine_ls_extinction_coef 0.0101(10)
_refine_ls_extinction_coef 0.0101(14)
_refine_ls_extinction_coef 0.0107(9)
_refine_ls_extinction_coef 0.0108(15)
_refine_ls_extinction_coef 0.0109(13)
_refine_ls_extinction_coef 0.011(2)
_refine_ls_extinction_coef 0.011(3)
_refine_ls_extinction_coef 0.0111(14)
_refine_ls_extinction_coef 0.0113(9)
_refine_ls_extinction_coef 0.0116(17)
_refine_ls_extinction_coef 0.0116(9)
_refine_ls_extinction_coef 0.0117(17)
_refine_ls_extinction_coef 0.0117(18)
_refine_ls_extinction_coef 0.0118(3)
_refine_ls_extinction_coef 0.0119(12)
_refine_ls_extinction_coef 0.0119(14)
_refine_ls_extinction_coef 0.0119(8)
_refine_ls_extinction_coef 0.012(2)
_refine_ls_extinction_coef 0.012(3)
_refine_ls_extinction_coef 0.0120(16)
_refine_ls_extinction_coef 0.0120(17)
_refine_ls_extinction_coef 0.0121(10)
_refine_ls_extinction_coef 0.0122(12)
_refine_ls_extinction_coef 0.0126(5)
_refine_ls_extinction_coef 0.013(2)
_refine_ls_extinction_coef 0.013(4)
_refine_ls_extinction_coef 0.0130(9)
_refine_ls_extinction_coef 0.0133(16)
_refine_ls_extinction_coef 0.0133(17)
_refine_ls_extinction_coef 0.0134(19)
_refine_ls_extinction_coef 0.0138(1)
_refine_ls_extinction_coef 0.014(3)
_refine_ls_extinction_coef 0.0145(12)
_refine_ls_extinction_coef 0.015(2)
_refine_ls_extinction_coef 0.015(3)
_refine_ls_extinction_coef 0.0152(8)
_refine_ls_extinction_coef 0.0159(19)
_refine_ls_extinction_coef 0.016(2)
_refine_ls_extinction_coef 0.016(3)
_refine_ls_extinction_coef 0.016(4)
_refine_ls_extinction_coef 0.017(2)
_refine_ls_extinction_coef 0.017(4)
_refine_ls_extinction_coef 0.017(5)
_refine_ls_extinction_coef 0.0173(4)
_refine_ls_extinction_coef 0.018(3)
_refine_ls_extinction_coef 0.0182(39)
_refine_ls_extinction_coef 0.0187(13)
_refine_ls_extinction_coef 0.0189(10)
_refine_ls_extinction_coef 0.019(2)
_refine_ls_extinction_coef 0.0213(13)
_refine_ls_extinction_coef 0.0213(19)
_refine_ls_extinction_coef 0.0216(7)
_refine_ls_extinction_coef 0.0217(12)
_refine_ls_extinction_coef 0.022(2)
_refine_ls_extinction_coef 0.022(4)
_refine_ls_extinction_coef 0.022(6)
_refine_ls_extinction_coef 0.023(3)
_refine_ls_extinction_coef 0.024(2)
_refine_ls_extinction_coef 0.024(4)
_refine_ls_extinction_coef 0.024(5)
_refine_ls_extinction_coef 0.025(2)
_refine_ls_extinction_coef 0.0251(11)
_refine_ls_extinction_coef 0.0261(16)
_refine_ls_extinction_coef 0.0271(17)
_refine_ls_extinction_coef 0.0274(16)
_refine_ls_extinction_coef 0.0275(12)
_refine_ls_extinction_coef 0.028(10)
_refine_ls_extinction_coef 0.028(7)
_refine_ls_extinction_coef 0.029(13)
_refine_ls_extinction_coef 0.030(4)
_refine_ls_extinction_coef 0.032(3)
_refine_ls_extinction_coef 0.032(5)
_refine_ls_extinction_coef 0.033(11)
_refine_ls_extinction_coef 0.033(3)
_refine_ls_extinction_coef 0.033(4)
_refine_ls_extinction_coef 0.034(4)
_refine_ls_extinction_coef 0.034(5)
_refine_ls_extinction_coef 0.034(9)
_refine_ls_extinction_coef 0.035(2)
_refine_ls_extinction_coef 0.036(10)
_refine_ls_extinction_coef 0.036(3)
_refine_ls_extinction_coef 0.0377(36)
_refine_ls_extinction_coef 0.038(3)
_refine_ls_extinction_coef 0.038(5)
_refine_ls_extinction_coef 0.039(8)
_refine_ls_extinction_coef 0.041(2)
_refine_ls_extinction_coef 0.041(9)
_refine_ls_extinction_coef 0.0416(20)
_refine_ls_extinction_coef 0.0433(12)
_refine_ls_extinction_coef 0.044(3)
_refine_ls_extinction_coef 0.044(4)
_refine_ls_extinction_coef 0.045(3)
_refine_ls_extinction_coef 0.046(3)
_refine_ls_extinction_coef 0.047(3)
_refine_ls_extinction_coef 0.049(11)
_refine_ls_extinction_coef 0.05(1)
_refine_ls_extinction_coef 0.050(6)
_refine_ls_extinction_coef 0.051(6)
_refine_ls_extinction_coef 0.052(5)
_refine_ls_extinction_coef 0.053(11)
_refine_ls_extinction_coef 0.053(3)
_refine_ls_extinction_coef 0.053(4)
_refine_ls_extinction_coef 0.054(11)
_refine_ls_extinction_coef 0.056(8)
_refine_ls_extinction_coef 0.058(2)
_refine_ls_extinction_coef 0.059(4)
_refine_ls_extinction_coef 0.062(5)
_refine_ls_extinction_coef 0.063(9)
_refine_ls_extinction_coef 0.064(3)
_refine_ls_extinction_coef 0.068(12)
_refine_ls_extinction_coef 0.068(3)
_refine_ls_extinction_coef 0.077(4)
_refine_ls_extinction_coef 0.08(2)
_refine_ls_extinction_coef 0.082(11)
_refine_ls_extinction_coef 0.083(4)
_refine_ls_extinction_coef 0.0889(30)
_refine_ls_extinction_coef 0.0920(50)
_refine_ls_extinction_coef 0.095(8)
_refine_ls_extinction_coef 0.099(7)
_refine_ls_extinction_coef 0.110(10)
_refine_ls_extinction_coef 0.117(7)
_refine_ls_extinction_coef 0.129(10)
_refine_ls_extinction_coef 0.129(5)
_refine_ls_extinction_coef 0.137(10)
_refine_ls_extinction_coef 0.147(9)
_refine_ls_extinction_coef 0.152(9)
_refine_ls_extinction_coef 0.164(8)
_refine_ls_extinction_coef 0.165(7)
_refine_ls_extinction_coef 0.166(17)
_refine_ls_extinction_coef 0.1770(182)
_refine_ls_extinction_coef 0.191(11)
_refine_ls_extinction_coef 0.204(10)
_refine_ls_extinction_coef 0.228(14)
_refine_ls_extinction_coef 0.238(4)
_refine_ls_extinction_coef 0.264(10)
_refine_ls_extinction_coef 0.324(9)
_refine_ls_extinction_coef 0.398(11)
_refine_ls_extinction_coef 0.61(10)
_refine_ls_extinction_coef 0.68(8)
_refine_ls_extinction_coef 1.45(3)
_refine_ls_extinction_coef 1070(45)
_refine_ls_extinction_coef 13(13)
_refine_ls_extinction_coef 13.2(4)
_refine_ls_extinction_coef 1317(348)
_refine_ls_extinction_coef 139(20)
_refine_ls_extinction_coef 15.9(15)
_refine_ls_extinction_coef 16.5(15)
_refine_ls_extinction_coef 16.860(4)
_refine_ls_extinction_coef 1630(119)
_refine_ls_extinction_coef 163E1(12)
_refine_ls_extinction_coef 17.4(3)
_refine_ls_extinction_coef 3.43(19)
_refine_ls_extinction_coef 3.91804
_refine_ls_extinction_coef 5.64E-7(6)
_refine_ls_extinction_coef 6.3(7)
_refine_ls_extinction_coef 6511(437)
_refine_ls_extinction_coef 6E-6(1)
_refine_ls_extinction_coef ?
_refine_ls_extinction_coef no
_refine_ls_extinction_coef none
_refine_ls_extinction_coef not_refined
I'm not quite sure where this leaves us in ensuring that we obtain
meaningful reports of extinction corrections.
Best wishes
Brian
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