# Re: comments on coreCIF.dic 2.1

• To: Multiple recipients of list <coredmg@iucr.org>
• Subject: Re: comments on coreCIF.dic 2.1
• From: Howard Flack <Howard.Flack@cryst.unige.ch>
• Date: Wed, 13 Jan 1999 17:23:12 GMT
```Comments (13th January 1999) on coreCIF.dic version 2.beta 5 by H.D.
Flack.

[Printed version received through the post from bm@iucr.org and
day. The two do not correspond exactly. I suspect that bm@iucr.org has
already implemented some of the typos indicated in David's message of
5th Jan. 1999]

Brian has done a very nice work putting all of the modifications into
place and David has been very scrupulous in his revision. I'll see
whether I have as many comments as he has. I examined in detail the
sections that interest me most and started at the end working backward
on the assumption that the others started at the beginning and worked
forward.

I am in full agreement with David's comments apart from as listed below:

>      'perpendicular component of the polarisation' is rather
>meaningless.  I assume what is meant is the 'electric vector of the
>major component of the polarisation'.

The expression is that of Azaroff and you find it in his book. Of
course it is confusing and difficult to explain in words but here goes.
Incident upon a reflecting plane (h k l) you have an incident and a
reflected ray. The three vectors comprising the incident ray direction,
the reflected ray direction and the normal to the reflecting plane are
co-planar and lie in what is called the diffraction plane. The vector
which is normal to the diffraction plane is necessarily perpendicular to
both the incident and the diffracted ray and moreover lies in (is
parallel to) the reflecting plane. Light polarised with an electric
vector parallel to the latter vector is called the parallel component of
the polarisation (because it is parallel to the reflecting plane) and
suffers no polarisation effect because it is easy to waggle the
electrons around parallel to the reflecting plane. The direction of
parallel polarisation of the incident beam is parallel to the direction
of parallel polarisation of the reflected beam (another reason for
calling them parallel). The other polarisation direction in the incident
and reflected rays is called the perpendicular component of
polarisation. They are perpendicular to the ray direction and the
parallel component of polarisation but the direction of perpendicular
polarisation in the incident beam and that in the reflected beam are not
in general either parallel or perpendicular one to another. Clear? I
doubt it!

>      This is quite a confusing definition.  I assume that what is
>meant is: 'The ratio of the intensities of the major polarisation
>component to the component perpendicular to this.  The direction of
>the electric vector of the major component is given in _*_norm.'

In fact the ratio is the way that Azaroff does things. As Syd
explained to me once and as is implemented in xtal thanks to the effort
of the late Ted Maslen, a ratio is not a good way to do things with
synchrotron radiation as a ratio may going shooting off to infinity. Ted
found that a fraction was a better way of doing things.
It seems to me that one needs advice from people using CIF and
synchrotron radiation before playing around with these definitions.

>13. _diffrn_refln_intensity_sigma
>    _diffrn_reflns_av_sigmaI/netI
>    _diffrn_reflns_class_av_sgI/I
>    _diffrn_standards_scale_sigma
>    _refine_ls_weighting_scheme
>    _reflns_threshold_expression
>    _reflns_shell_meanI_over_sigI_ (two data items)
>      There is an element of confusion in these data definitions.
> We have replaced the ambiguous e.s.d. by s.u.

I do not agree with David's interpretation.
sigma should be reserved for the square root of the variance of a
probability density function. It is a theoretical value, unknowable and
unmeasurable.
(Standard) uncertainties are experimentally-determined values, or
values taken from prior information, or a combination of the two.
Indeed experimental values in CIF should not mention sigma or sigmaI
or sigI or sgI (especially in such variety) but should only use some
uniform way of abreviating 'standard uncertainty' in the text and in the
data names. Hardly surprisingly the last time I suggested this there was
very little enthusiasm for its implementation.

>14. _diffrn_refln_scan_width
>      Is this angle measured as theta or 2*theta?  I assume 2*theta,
I assume omega since this is the only one which is sure to scan. But
I agree that the definiton should make it clear. It would seem to me
that _diffrn_refln_scan_rate needs clarifying in the same way.

>18. _diffrn_reflns_number
>    _diffrn_reflns_class_number

>or because they are the result of
>glide planes and screw axes.  The latter are also elements of
>'translational symmetry'
I do not agree. They are symmetry operations with a translational
component.

(1) data_atom_site_U_iso_or_equiv
U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ A~i~.A~j~)] has a
. that it should not have.

(2) data_chemical_[]
needs a means to record enantioselective chromatography results to
prove enantiopurity. The _formula_ may need something more specific
concerning (+-) rac- and racem-. Expect to be hearing from me when I
have a specific suggestion.

(3) data_diffrn_measured_fraction_theta_full
Should not    _enumeration_range    0:1.0 really be 0.95:1.0 since
_diffrn_reflns_theta_full mentions 'nearly complete'. 0.0 or 0.5 do not
seem 'nearly complete' to me!?

(4) data_diffrn_refln_[]
I suggest either adding parentheses in the definition or omitting
the part that I have now put in parentheses:

_definition
;              Data items in the DIFFRN_REFLN category record details
the intensities measured in the diffraction experiment.

The DIFFRN_REFLN data items refer to individual intensity
measurements, and must be included in looped lists.

(The DIFFRN_REFLNS data items specify the parameters that
apply
to all intensity  measurements. The DIFFRN_REFLNS data
items
are not looped.)
;

(5)   '_diffrn_refln_counts_net'
Net counts can go negative so  _enumeration_range           0: is
wrong.

(6)  data_diffrn_reflns_[]
I suggest either rearranging and adding parentheses in the
definition or omitting the part that I have now put in parentheses:
_definition
;              Data items in the DIFFRN_REFLNS category record details
the set of intensities measured in the diffraction
experiment.

The DIFFRN_REFLNS data items specify the parameters that
apply
to all intensity measurements. The DIFFRN_REFLNS data
items
are not looped.

(The DIFFRN_REFLN data items refer to individual
intensity
measurements, and must be included in looped lists.)

(7) data_diffrn_reflns_av_R_equivalents
The definition should be
_definition
;              The residual [sum av|del(I)| / sum|av(I)|] for
symmetry-equivalent
reflections used to calculate the average intensity
av(I). The
av|del(I)| term is the average absolute difference
between av(I) and
the individual symmetry-equivalent intensities.
;
because the average of del I is zero by definition.
data_diffrn_reflns_class_av_R_eq has the same problem.

(8) data_diffrn_reflns_av_sigmaI/netI
Apart from hating the 'sigmaI', the definition should be
_definition
;              Measure [sum u(netI)/sum|netI|] for all measured
reflections.
;
data_diffrn_reflns_class_av_sgI/I has the same problem.

(9) data_diffrn_reflns_theta_full
Remove diffractometer as second word in the definition:
;              The theta angle (in degrees) at which the
measured reflection count is close to complete. The
fraction
of unique reflections measured out to this angle is given
by
_diffrn_measured_fraction_theta_full.
;

(10) data_diffrn_reflns_class_number

(11) data_exptl_crystal_F_000

external e-mail. As the Acta Cryst C not longer requires F000 to be
given, the only interest in this item was from George for use in files
which communicate to electron density calculation programmes (Fourier
programs). In which case, according to me, there are two values worthy
of being communicated: (1) the electron count concerning the total
electron content of the unit cell as known from chemical analysis and
other prior information and (2) the electron count  concerning the total
number of electrons per unit cell introduced into the model. Neither
should have dispersion contributions.

(12) data_refine_diff_density_
The definition would be better as:
_definition
;              The largest, smallest and root-mean-square-deviation, in
electrons per angstrom cubed, of the final difference
electron
density. The *_rms value is measured with
respect to the arithmetic mean density, and is derived
from
summations over each grid point in the asymmetric unit of
the cell. This quantity is useful for assessing the
significance of *_min and *_max values, and also for
defining suitable contour levels.

(13)  data_refine_ls_abs_structure_details
Remove  'For example, it may describe the Friedel pairs used.'
from the definition as this is much better described now by
data_reflns_Friedel_coverage.

(14) data_refine_ls_goodness_of_fit_all
data_refine_ls_goodness_of_fit_gt
data_refine_ls_goodness_of_fit_ref

In the formulae, there are 4 | characters. In principle these should
be parentheses or square brackets.

(15) data_refine_ls_restrained_S_all
data_refine_ls_restrained_S_gt

(a) the |s should be parentheses or square brackets.
(b) more serious, in the print version, the square root is not
applied to the denominator. Is this due to ( ) instead of { } in the
.dic file of the formulae?

(16) data_refine_ls_wR_factor_all
data_refine_ls_wR_factor_gt
data_refine_ls_wR_factor_ref
data_refine_ls_class_wR_factor_all
data_reflns_class_wR_factor_all   (Looks as though bm@iucr.org has
already got the last two but he has put in many | that have no place
there.  This reminds me of the days when both I and Glauser update CWW
Whats New. We manage to erase each others postings!)

The term in the denominator should be Y(obs) not Y(calc)

(17)  data_refln_symmetry_multiplicity
In the definition remove ' and the Friedel relationship' to give:
_definition
;              The number of symmetry-equivalent reflections. The
equivalent
reflections have the same structure-factor magnitudes
because
of the space-group symmetry.
;
There is no case for adding in a centre of symmetry. h k l and -h
-k -l do not have the same Fs in a non-centrosymmetric space group.

(18)  data_reflns_special_details
In definition remove 'It should include details of the Friedel
pairs.'. This is much better treated by data_reflns_Friedel_coverage.

(19)  data_reflns_class_number_gt
_definition
;              For each reflection class, the number of significantly
intense
reflections (see _reflns_threshold_expression) in the
_refln_
list (not the _diffrn_refln_ list). It may include
Friedel
equivalent reflections (i.e. those which are
symmetry equivalent under the Laue symmetry but
inequivalent
under the crystal class) according to the nature of the
structure
and the procedures used. The item _reflns_special_details
describes the reflection data.
;

(20) data_reflns_class_R_Fsqd_factor
Typos. 4 spaces around the = , squared amplitudes instead of
squares, no || in the denominator.

_definition
;              For each reflection class, the residual factor R(F^2^)
calculated
on the squared amplitudes of the observed and calculated
structure
factors,
for the reflections judged significantly intense (i.e.
satisfying
the threshold specified by _reflns_threshold_expression)
and
included in the refinement. The reflections also satisfy
the
resolution limits established by _reflns_class_d_res_high
and
_reflns_class_d_res_low.
R(F^2^)=sum|F(obs)^2^-F(calc)^2^|/sumF(obs)^2^
F(obs)^2^ = squares of the observed structure-factor
amplitudes,
F(calc)^2^ = squares of the calculated structure-factor
amplitudes,
and the sum is taken over the specified reflections.
;

(21)  And now I'm really fed up and need to drink a beer.  It snowed
like mad in town last night.

Best wishes and a belated Happy New Year to you all.

H.
--
Howard Flack        http://www.unige.ch/crystal/ahdf/Howard.Flack.html
Laboratoire de Cristallographie               Phone: 41 (22) 702 62 49
24 quai Ernest-Ansermet             mailto:Howard.Flack@cryst.unige.ch
CH-1211 Geneva 4, Switzerland                   Fax: 41 (22) 702 61 08
```

[Send comment to list secretary]