[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

# New version of CIF Core dictionary (2.4)

*To*:*comcifs@iucr.org***Subject**:**New version of CIF Core dictionary (2.4)****From**:**Brian McMahon <bm@iucr.org>***Date*:*Tue, 18 Dec 2007 10:06:13 +0000*

Dear COMCIFS The Core Dictionary Management Group proposes a number of additions to the core dictionary and a few minor revisions to existing content, and requests the voting members of COMCIFS to approve these changes. The changes are summarised below (the additional data items are listed explicitly). The discussions of the coreDMG are available at http://www.iucr.org/iucr-top/lists/coredmg/index.html This draft has been approved following technical review by the Dictionary Review Committee, who recommend that COMCIFS formally approve this release. All members of this mailing list are welcome to comment on the draft, but VOTING MEMBERS (I. D. Brown, H. M. Berman, H. J. Bernstein, R. W. Grosse-Kunstleve, S. R. Hall, G. Madariaga, B. McMahon and J. Westbrook) ARE REQUIRED TO SUBMIT A FORMAL VOTE for or against the new version. PLEASE SUBMIT YOUR VOTE BY JANUARY 20th 2008. A complete draft of the dictionary incorporating these revisions may be inspected at ftp://ftp.iucr.org/cifdics/draft_cif_core_2.4.dic with formatted versions (PDF and HTML respectively) at ftp://ftp.iucr.org/cifdics/draft_core2.4.pdf http://www.iucr.org/iucr-top/cif/cifdic_html/1/cif_core_draft2.4.dic/index.html If this version is approved, the relevant Chapters of International Tables for Crystallography Volume G (Online) will be updated to reflect and describe the new content. Best wishes Brian McMahon Coordinating Secretary #======================================================================== PROPOSED CHANGES IN CIF CORE DICTIONARY VERSION 2.4 2007-12-04 BMcM: Fixed typo in equation appearing in _diffrn_reflns_av_sigmaI/netI and _diffrn_reflns_av_unetI/netI 2007-12-04 IDB: Added new items approved by coreDMG: SUMMARY 1. _atom_sites_solution_ Added new flags notdet, dual, other (Bruce Noll) 2. _chemical_enantioexcess_ Added items *_bulk, *_bulk_technique, *_crystal, *_crystal_technique (H. D. Flack) 3. _diffrn_..._measured_fraction_ Added sentences to definitions of _diffrn_reflns_resolution_full, *_theta_max and *_resolution_max. Added new data items _diffrn_reflns_Laue_measured_fraction_full, *_max _diffrn_reflns_point_group_measured_fraction_full and *_max 4. _diffrn_standards_decay_% Clarified definition and added examples. 5. _distributed_density_ Added _atom_site_distributed_density_id and the new DISTRIBUTED_DENSITY category following suggestions from David Watkin. 6. _exptl_absorption_correction_T_max, *_T_min Clarified definition and added items exptl_transmission_factor_max and *_min 7. _geom_bond_multiplicity New data item added. 8. _publ_section_keywords New data name added. 9. _refine_ls_F_calc Added _refine_ls_F_calc_details, *_formula and *_precision. 10. _symmetry_equiv Added _enumeration_default 1 to _space_group_symop_id and _symmetry_equiv_pos_site_id; added _enumeration_default x,y,z to _symmetry_equiv_pos_as_xyz; added comment about the need to have the identity as symop 1 to _space_group_symop_operation_xyz, _space_group_symop_id, _symmetry_equiv_pos_as_xyz and _symmetry_equiv_pos_site_id #------------------------------------------------------------------------ PROPOSED NEW DATA ITEMS: #------------------------------------------------------------------------ data_atom_site_distributed_density_id _name '_atom_site_distributed_density_id' _category atom_site _type char _list yes _list_reference '_atom_site_label' _list_mandatory no _list_link_parent '_distributed_density_id' _example an1 _example_detail 'see example in category DISTRIBUTED_DENSITY' _definition ; An identifier that links the atom defined by _atom_site_label with the distributed density of this atom defined in the DISTRIBUTED_DENSITY category. Note that all the atoms that give rise to a particular distributed density, e.g. a ring, should be included in the ATOM_SITE list, even when they, or the centroid of the distribution, lie on a special position. That is, the crystallographic site symmetry of the distribution is not used to generate the full distributed density shape from the crystallographic asymmetric portion. The value of _atom_site_symmetry_multiplicity should be chosen so that for each of the atoms in the ATOM_SITE list (_atom_site_occupancy)*(_atom_site_symmetry_multiplicity) is equal to its contribution to (_chemical_formula_sum)*(_cell_formula_units_Z). ; data_chemical_enantioexcess_bulk _name '_chemical_enantioexcess_bulk' _category chemical _type numb _type_conditions esd _enumeration_range 0.0:1.0 _units . _units_detail dimensionless _definition ; The enantioexcess of the bulk material from which the crystals were grown. A value of 0.0 indicates the racemate. A value of 1.0 indicates that the compound is enantiomerically pure. Enantioexcess is defined in the IUPAC Recommendations (Moss et al., 1996). The composition of the crystal and bulk must be the same. Ref: Moss G. P. et al. (1996). Basic Terminology of Stereochemistry. Pure Appl. Chem., 68, 2193-2222. http://www.chem.qmul.ac.uk/iupac/stereo/index.html ; data_chemical_enantioexcess_bulk_technique _name '_chemical_enantioexcess_bulk_technique' _category chemical _type char loop_ _enumeration _enumeration_detail OA ; Enantioexcess determined by measurement of the specific rotation of the optical activity of the bulk compound in solution. ; CD ; Enantioexcess determined by measurement of the visible/near UV circular dichroism spectrum of the bulk compound in solution. ; EC ; Enantioexcess determined by enantioselective chromatography of the bulk compound in solution. ; other ; Enantioexcess determined by a technique not included elsewhere in this list. ; _definition ; The experimental technique used to determine the enantioexcess of the bulk compound. ; data_chemical_enantioexcess_crystal _name '_chemical_enantioexcess_crystal' _category chemical _type numb _type_conditions esd _enumeration_range 0.0:1.0 _units . _units_detail dimensionless _definition ; The enantioexcess of the crystal used for the diffraction study. A value of 0.0 indicates the racemate. A value of 1.0 indicates that the crystal is enantiomerically pure. Enantioexcess is defined in the IUPAC Recommendations (Moss et al., 1996). Ref: Moss G. P. et al. (1996). Basic Terminology of Stereochemistry. Pure Appl. Chem., 68, 2193-2222. http://www.chem.qmul.ac.uk/iupac/stereo/index.html ; data_chemical_enantioexcess_crystal_technique _name '_chemical_enantioexcess_crystal_technique' _category chemical _type char loop_ _enumeration _enumeration_detail CD ; Enantioexcess determined by measurement of the visible/near UV circular dichroism spectrum of the crystal taken into solution. ; EC ; Enantioexcess determined by enantioselective chromatography of the crystal taken into solution. ; other ; Enantioexcess determined by a technique not included elsewhere in this list. ; _definition ; The experimental technique used to determine the enantioexcess of the crystal. ; data_diffrn_reflns_Laue_measured_fraction_full _name '_diffrn_reflns_Laue_measured_fraction_full' _category diffrn_reflns _type numb _related_item '_diffrn_measured_fraction_theta_full' _related_function alternate _enumeration_range 0.95:1.0 _definition ; Fraction of Laue unique reflections (symmetry-independent in the Laue group) measured out to the resolution given in _diffrn_reflns_resolution_full or _diffrn_reflns_theta_full. The Laue group always contains a centre of symmetry so that the reflection h,k,l is always equivalent to the reflection -h,-k,-l even in space groups without a centre of symmetry. This number should not be less than 0.95, since it represents the fraction of reflections measured in the part of the diffraction pattern that is essentially complete. ; data_diffrn_reflns_Laue_measured_fraction_max _name '_diffrn_reflns_Laue_measured_fraction_max' _category diffrn_reflns _type numb _related_item '_diffrn_measured_fraction_theta_max' _related_function alternate _enumeration_range 0:1.0 _definition ; Fraction of Laue unique reflections (symmetry-independent in the Laue group) measured out to the resolution given in _diffrn_reflns_resolution_max or _diffrn_reflns_theta_max. The Laue group always contains a centre of symmetry so that the reflection h,k,l is always equivalent to the reflection -h,-k,-l even in space groups without a centre of symmetry. ; data_diffrn_reflns_point_group_measured_fraction_full _name '_diffrn_reflns_point_group_measured_fraction_full' _category diffrn_reflns _type numb _related_item '_diffrn_measured_fraction_theta_full' _related_function alternate _enumeration_range 0.95:1.0 _definition ; Fraction of crystal point-group unique reflections (i.e. symmetry-independent in the crystal point group) measured out to the resolution given in _diffrn_reflns_resolution_full or _diffrn_reflns_theta_full. For space groups that do not contain a centre of symmetry the reflections h,k,l and -h,-k,-l are independent. This number should not be less than 0.95, since it represents the fraction of reflections measured in the part of the diffraction pattern that is essentially complete. ; data_diffrn_reflns_point_group_measured_fraction_max _name '_diffrn_reflns_point_group_measured_fraction_max' _category diffrn_reflns _type numb _related_item '_diffrn_measured_fraction_theta_max' _related_function alternate _enumeration_range 0:1.0 _definition ; Fraction of crystal point-group unique reflections (i.e. symmetry-independent in the crystal point group) measured out to the resolution given in _diffrn_reflns_resolution_max or _diffrn_reflns_theta_max. For space groups that do not contain a centre of symmetry the reflections h,k,l and -h,-k,-l are independent. ; reflection count is close to complete. The fraction of unique reflections measured out to this angle is given by _diffrn_measured_fraction_theta_full. diffraction pattern. The fraction of unique reflections measured out to this angle is given by _diffrn_measured_fraction_theta_max The fraction of unique reflections measured out to this angle is given by _diffrn_measured_fraction_theta_max ######################### ## DISTRIBUTED_DENSITY ## ######################### data_distributed_density_[] _name '_distributed_density_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_adp_type _atom_site_distributed_density_id _atom_site_calc_flag # Inner ring of cyclopentadiene carbon atoms and borazole C1 C -0.1362(8) -0.0974(8) -0.3116(10) 0.0662(18) 0.625(1) 4 Uiso . d C2 C -0.1060(8) -0.2165(8) -0.1837(10) 0.071(2) 0.625(1) 4 Uiso . d C3 C -0.1774(9) -0.1939(9) -0.0820(11) 0.082(2) 0.625(1) 4 Uiso . d C4 C -0.2529(9) -0.0561(9) -0.1479(12) 0.084(2) 0.625(1) 4 Uiso . d C5 C -0.2261(8) -0.0002(8) -0.2891(10) 0.072(2) 0.625(1) 4 Uiso . d C1a C . . . . 0.208(1) 4 . an1 dum C2a C . . . . 0.208(1) 4 . an1 dum C3a C . . . . 0.208(1) 4 . an1 dum C4a C . . . . 0.208(1) 4 . an1 dum C5a C . . . . 0.208(1) 4 . an1 dum N1 N -0.1375(8) -0.0968(8) -0.3201(10) 0.065(2) 0.167(1) 4 Uiso . d B1 B -0.1002(8) -0.2265(8) -0.1728(10) 0.071(2) 0.167(1) 4 Uiso . d N2 N -0.1402(8) -0.1034(8) -0.0765(10) 0.076(2) 0.167(1) 4 Uiso . d B2 B -0.2370(9) -0.0364(9) -0.1832(10) 0.085(2) 0.167(1) 4 Uiso . d N3 N -0.2893(8) 0.0034(8) -0.3621(10) 0.062(2) 0.167(1) 4 Uiso . d B3 B -0.2246(9) -0.0452(9) -0.3004(11) 0.073(2) 0.167(1) 4 Uiso . d # Outer ring of methyl groups C11 C -0.0951 -0.0733 -0.4330 0.1901 0.625(1) 4 Uani . d C12 C -0.0272 -0.3236 -0.1750 0.1990 0.625(1) 4 Uani . d C13 C -0.1719 -0.2833 0.0404 0.2483 0.625(1) 4 Uani . d C14 C -0.3291 -0.0080 -0.0844 0.2450 0.625(1) 4 Uani . d C15 C -0.2817 0.1218 -0.3770 0.2219 0.625(1) 4 Uani . d C11a C . . . . 0.208(1) 4 . an2 dum C12a C . . . . 0.208(1) 4 . an2 dum C13a C . . . . 0.208(1) 4 . an2 dum C14a C . . . . 0.208(1) 4 . an2 dum C15a C . . . . 0.208(1) 4 . an2 dum # Details of the two rings of distributed density are given # in the following loop loop_ _distributed_density_id _distributed_density_shape _distributed_density_position_x _distributed_density_position_y _distributed_density_position_z _distributed_density_radius _distributed_density_direction_h _distributed_density_direction_k _distributed_density_direction_l _distributed_density_Uiso _distributed_density_symmetry_multiplicity an1 ring -0.1810(8) -0.1133(8) -0.2058(8) 1.198(6) 1.35(2) 0.07(2) -0.45(2) 0.052(2) 4 an2 ring -0.1873(14) -0.1156(14) -0.2210(2) 2.626(6) 1.30(2) 0.10(2) -0.40(2) 0.131(3) 4 ; ; Example 1 - This example is fictitious (and chemically implausible) but it is designed to illustrate how a complex system of distributed density can be recorded. In this example pentamethyl cyclopentadiene (Cp*) and borazole occupy the same location in the crystal in the ratio 5:1. The atoms of the borazole ring are fixed as are three quarters of the atoms in the Cp* ring, but the remaining quarter of the Cp* molecules are freely rotating around the cylindrical Cp* axis. The rotating Cp* molecules give rise to two concentric rings of density, one from the atoms in the ring and the other from the methyl groups (hydrogen atoms are ignored). On top of these rings lie the atoms of the fixed Cp* molecules. The atoms of the borazole molecule also lie over the inner Cp* ring. Full details of the chemical composition are given in the ATOM_SITE loop together with the positions of the fixed atoms. The coordinates of the atoms that give rise to the distributed ring of density are set to '.', meaning that they have no significance as the atoms are dummy atoms. They are included to give the correct composition when _atom_site_occupancy and _atom_site_symmetry_multiplicity are given. The composition defined in the ATOM_SITE loop is linked to the DISTRIBUTED_DENSITY loop through the parent-child identifiers, 'an1' and 'an2' (for annulus 1 and 2). The one quarter of the Cp* molecules that are rotating have the occupation number of 0.208 = 2/24 = 5/6 (the total occupancy of the Cp*) x 1/4 (the portion rotating). The three quarters that are in fixed positions have the occupation number of 0.625 = 15/24 = 5/6 x 3/4. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the distributed_density category describe the geometric arrangement of an atom or atoms when they are distributed uniformly over a line or surface such as a ring, cylindrical shell or spherical shell, the line or surface being given a thickness through the application of an atomic displacement parameter. ; data_distributed_density_details _name '_distributed_density_details' _category distributed_density _type char _list both _list_reference '_distributed_density_id' _example ; The distribution was modelled using a disc of density of the given radius. ; _definition ; Information about the distribution of density not given in other items. ; data_distributed_density_direction_ loop_ _name '_distributed_density_direction_h' '_distributed_density_direction_k' '_distributed_density_direction_l' _category distributed_density _type numb _type_conditions esd _list both _list_reference '_distributed_density_id' _units rlu _units_detail 'reciprocal lattice units' _definition ; The (covariant) components on a reciprocal-lattice basis of a vector of arbitrary length used to indicate the direction of the unique axis of the distribution, e.g. the axis of a cylindrical shell or the normal to the plane of a ring. ; data_distributed_density_id _name '_distributed_density_id' _category distributed_density _type char _list both _list_mandatory yes _list_link_child '_atom_site_distributed_density_id' _definition ; An identifier that links the atom defined by _atom_site_label with a distributed density defined in the DISTRIBUTED_DENSITY category. ; data_distributed_density_length _name '_distributed_density_length' _category distributed_density _type numb _type_conditions esd _list both _list_reference '_distributed_density_id' _enumeration_range 0.0: _units A _units_detail 'Angstrom units' _definition ; The length of the line or cylindrical shell of distributed density in angstroms. ; data_distributed_density_position_ loop_ _name '_distributed_density_position_x' '_distributed_density_position_y' '_distributed_density_position_z' _category distributed_density _type numb _type_conditions esd _list both _list_reference '_distributed_density_id' _definition ; The position of the centroid of the distributed density in fractions of the unit cell values. ; data_distributed_density_radius _name '_distributed_density_radius' _category distributed_density _type numb _type_conditions esd _list both _list_reference '_distributed_density_id' _enumeration_range 0.0: _units A _units_detail 'Angstrom units' _definition ; The radius of the ring, or of the cylindrical or spherical shell, of distributed density in angstroms. ; data_distributed_density_shape _name '_distributed_density_shape' _category distributed_density _type char _list both _list_reference '_distributed_density_id' loop_ _enumeration _enumeration_detail line 'line segment' infline ; infinite line running through the crystal ; ring 'circular ring' cylshell ; cylindrical shell of finite length ; infcylshell ; cylindrical shell running through the crystal ; sphereshell 'spherical shell' other ; give details in _distributed_density_details ; _definition ; A flag that indicates the shape of the distributed density. The lines and ring are one-dimensional distributions of atoms and the cylindrical shell and spherical shell are two-dimensional distributions. In each case the root-mean-square thickness of the distribution is given by the atomic displacement parameter defined in _distributed_density_Uiso. ; data_distributed_density_symmetry_multiplicity _name '_distributed_density_symmetry_multiplicity' _category distributed_density _type numb _list both _list_reference '_distributed_density_id' _enumeration_range 1:192 _definition ; The number of images of the centroid of the distributed density that the space-group symmetry generates in the unit cell reported in the CELL category. It is the number that appears in International Tables for Crystallography Vol. A (2002) for the Wyckoff position occupied by the centroid. In this treatment the symmetry of the distribution itself is ignored, including any operations of its point group that are part of the crystallographic site symmetry of the centroid. All the atoms that give rise to the distributed density should therefore be listed in the ATOM_SITE category even if they, or the centroid of the distribution, lie on crystallographic special positions. For example, if the distribution is a ring and the centroid of the ring lies on a crystallographic mirror plane, all the atoms in the ring are listed if the ring lies either in or perpendicular to the mirror plane since the mirror image of the ring lies over the ring itself. If the ring is at some arbitrary angle to the mirror plane, the mirror generates a second ring and both rings should be described independently. However, because both rings cannot be simultaneously occupied, the occupation numbers given in the ATOM_SITE category must have a value equal to or less than 0.5. ; data_distributed_density_Uiso _name '_distributed_density_Uiso' _category distributed_density _type numb _type_conditions esd _list both _list_reference '_distributed_density_id' _enumeration_range 0.0: _units A^2^ _units_detail 'Angstrom units squared' _example 0.018(3) _definition ; The factor exp(-Ux^-2^) is applied to all parts of the distribution, where U = _distributed_density_Uiso and x is the distance from the ideal one- or two-dimensional shape. This emulates the effects of thermal motion or static displacement from the ideal positions described in this category and has the effect of converting the simple one- or two-dimensional geometric shapes into three-dimensional objects of mean square thickness U. ; data_exptl_transmission_factor_max _name '_exptl_transmission_factor_max' _category exptl _type numb _type_conditions su _enumeration_range 0.0:1.0 _definition ; The calculated maximum value of the transmission factor for the specimen. Its value does not include the effects of absorption in the specimen mount. The presence of this item does not imply that the structure factors have been corrected for absorption. The applied correction should be given by _exptl_absorpt_correction_T_max. ; data_exptl_transmission_factor_min _name '_exptl_transmission_factor_min' _category exptl _type numb _type_conditions su _enumeration_range 0.0:1.0 _definition ; The calculated minimum value of the transmission factor for the specimen. Its value does not include the effects of absorption in the specimen mount. The presence of this item does not imply that the structure factors have been corrected for absorption. The applied correction should be given by _exptl_absorpt_correction_T_min. ; data_geom_bond_multiplicity _name '_geom_bond_multiplicity' _category geom_bond _type numb _list yes _list_reference '_geom_bond_atom_site_label_' _enumeration_range 0: _enumeration_default 1 _definition ; The number of times the given bond appears in the environment of the atoms labelled _geom_bond_atom_site_label_1. In cases where the full list of bonds is given, one of the series of equivalent bonds may be assigned the appropriate multiplicity while the others are assigned a value of 0. ; data_refine_ls_F_calc_details _name '_refine_ls_F_calc_details' _category refine _type char loop_ _example 'Gaussian integration using 16 points' ; Bessel functions expansion up to 5th order. Bessel functions estimated accuracy: better than 0.001 electrons. ; _definition ; Details concerning the evaluation of the structure factors using the expression given in _refine_ls_F_calc_formula. ; data_refine_ls_F_calc_formula _name '_refine_ls_F_calc_formula' _category refine _type char _definition ; Analytical expression used to calculate the structure factors. ; data_refine_ls_F_calc_precision _name '_refine_ls_F_calc_precision' _category refine _type numb _enumeration_range 0.0: _definition ; This item gives an estimate of the precision resulting from the numerical approximations made during the evaluation of the structure factors using the expression given in _refine_ls_F_calc_formula following the method outlined in _refine_ls_F_calc_details. For X-ray diffraction the result is given in electrons. ; #======================================================================== _______________________________________________ comcifs mailing list comcifs@iucr.org http://scripts.iucr.org/mailman/listinfo/comcifs

**Reply to: [list | sender only]**

- Prev by Date:
**Re: COMCIFS program for Osaka** - Next by Date:
**COMCIFS annual report to the IUCr Executive** - Prev by thread:
**COMCIFS annual report to the IUCr Executive** - Next by thread:
**Re: New version of CIF Core dictionary (2.4)** - Index(es):