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# 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 downloaded from ftp://ftp.iucr.org/cifdics/cif_core_2.1beta5.dic this 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: >10. _diffrn_radiation_polarisn_norm > '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! >11. _diffrn_radiation_polarisn_ratio > 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. Now my own comments: (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 about 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 about 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 Absences not extinctions please. (11) data_exptl_crystal_F_000 There was some discussion in coredmg about this one due to an 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 Add parenthetical phrase to definiton. _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

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