Non-defined datnames being used in published CIFs

Discussion of core CIF dictionary definitions. Please choose topic headings so that the first words refer to a particular dataname or category, whether existing or proposed.

Non-defined datnames being used in published CIFs

Postby Tony_Linden » Fri Mar 28, 2014 10:04 am

Dear Colleagues,

This thread seems to be getting off to a slow start. Perhaps people don't really know what needs to be done.

I include below for consideration a scratched-together rough list of all small-molecule single-crystal CIF unofficial undefined datanames that are currently in use by various software packages or in Chester processed publications. The list might not be exhaustive, but shows the trend developing because of the absence of suitable datanames in the CIF dictionary to cover some things that are done routinely now, but were perhaps non-existent when CIF was originally released. The list here does not include any other things that maybe it would be good to have definitions for (e.g. absorption correction Tmin/Tmax is currently used to record the total corrections to the data, whereas in reality this is a combination of many corrections (scaling, absorption, etc.), or any exiting official items that we need to update definitions for or the underlying list of keywords for. If I find time, I might try to make these lists.

My feeling is that we should try to unify the definitions being used by various programs into a common basis. In doing so, things should be as practical for users as possible, so whatever we define should not deviate from the current usage as far as is avoidable. Otherwise, convincing programmers to adopt our recommendations will be nigh on impossible.

Cheers,
Tony Linden
anthony.linden@chem.uzh.ch


List of New & officially undefined Datanames
============================================

Definition needed for Z'.

SHELX (needing dictionary info/definitions)

_shelx_title
_shelx_refln_list_code
_shelx_F_calc_maximum
_shelx_refinement_sigma (incluses weighting scheme - might be generalized)

_shelx_space_group_comment
_shelx_estimated_absorpt_T_min
_shelx_estimated_absorpt_T_max
_shelx_version_number
_shelx_res_file
_shelx_res_checksum
_shelx_hkl_file
_shelx_hkl_checksum
_shelx_fab_file
_shelx_fab_checksum


PLATON (SQUEEZE)

_platon_squeeze_void_nr
_platon_squeeze_void_average_x
_platon_squeeze_void_average_y
_platon_squeeze_void_average_z
_platon_squeeze_void_volume
_platon_squeeze_void_count_electrons
_platon_squeeze_void_content
_platon_squeeze_details


OLEX2 (SQUEEZE)

_smtbx_masks_special_details
_smtbx_masks_void_nr
_smtbx_masks_void_average_x
_smtbx_masks_void_average_y
_smtbx_masks_void_average_z
_smtbx_masks_void_volume
_smtbx_masks_void_count_electrons
_smtbx_masks_void_content
_Olex2_refine_description
_olex2_refinement_description

AGILENT
(Agilent defined datanames)
(the following used to report the cell refined without symmetry constraints applied, while the true constrained cell is reported under the "normal" items.)
_cell_oxdiff_length_a
_cell_oxdiff_length_b
_cell_oxdiff_length_c
_cell_oxdiff_angle_alpha
_cell_oxdiff_angle_beta
_cell_oxdiff_angle_gamma
_cell_oxdiff_volume
_cell_oxdiff_measurement_reflns_used 16529
_reflns_odcompleteness_completeness 99.98
_reflns_odcompleteness_theta 66.97
_reflns_odcompleteness_iscentric 1
_chemical_oxdiff_formula 'C27 H30 Cl2 N2 O3 S'

_cell_oxdiff_twin_number 2
loop_
_cell_oxdiff_twin_id
_cell_oxdiff_twin_matrix_11
_cell_oxdiff_twin_matrix_12
_cell_oxdiff_twin_matrix_13
_cell_oxdiff_twin_matrix_21
_cell_oxdiff_twin_matrix_22
_cell_oxdiff_twin_matrix_23
_cell_oxdiff_twin_matrix_31
_cell_oxdiff_twin_matrix_32
_cell_oxdiff_twin_matrix_33
1 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000
2 -0.9999 -0.0001 0.0002 0.0023 -1.0005 -0.0017 0.6363 -0.0011 0.9995

loop_
_diffrn_oxdiff_twin_id
_diffrn_oxdiff_twin_ratio
_diffrn_oxdiff_twin_reflns_isolated
_diffrn_oxdiff_twin_reflns_overlapped
1 0.4419 2610 39599
2 0.5581 2626 39599

RIGAKU
(Rigaku defined datanames)

JANA
loop_
_jana_cell_twin_matrix_id
_jana_cell_twin_volume_fraction
_jana_cell_twin_matrix_1_1
_jana_cell_twin_matrix_1_2
_jana_cell_twin_matrix_1_3
_jana_cell_twin_matrix_2_1
_jana_cell_twin_matrix_2_2
_jana_cell_twin_matrix_2_3
_jana_cell_twin_matrix_3_1
_jana_cell_twin_matrix_3_2
_jana_cell_twin_matrix_3_3
1 0.797(6)
1 0 0
0 1 0
0 0 1
2 0.203(6)
-1 0 0
0.4715 -0.0035 1.0035
0.4715 0.9965 0.0035
loop_
_jana_atom_site_ADP_C_label
_jana_atom_site_ADP_C_type_symbol
_jana_atom_site_ADP_C_111
_jana_atom_site_ADP_C_112
_jana_atom_site_ADP_C_113
_jana_atom_site_ADP_C_122
_jana_atom_site_ADP_C_123
_jana_atom_site_ADP_C_133
_jana_atom_site_ADP_C_222
_jana_atom_site_ADP_C_223
_jana_atom_site_ADP_C_233
_jana_atom_site_ADP_C_333
? ? ? ? ? ? ? ? ? ? ? ?

loop_
_jana_atom_site_ADP_D_label
_jana_atom_site_ADP_D_type_symbol
_jana_atom_site_ADP_D_1111
_jana_atom_site_ADP_D_1112
_jana_atom_site_ADP_D_1113
_jana_atom_site_ADP_D_1122
_jana_atom_site_ADP_D_1123
_jana_atom_site_ADP_D_1133
_jana_atom_site_ADP_D_1222
_jana_atom_site_ADP_D_1223
_jana_atom_site_ADP_D_1233
_jana_atom_site_ADP_D_1333
_jana_atom_site_ADP_D_2222
_jana_atom_site_ADP_D_2223
_jana_atom_site_ADP_D_2233
_jana_atom_site_ADP_D_2333
_jana_atom_site_ADP_D_3333
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

loop_
_jana_atom_site_ADP_E_label
_jana_atom_site_ADP_E_type_symbol
_jana_atom_site_ADP_E_11111
_jana_atom_site_ADP_E_11112
_jana_atom_site_ADP_E_11113
_jana_atom_site_ADP_E_11122
_jana_atom_site_ADP_E_11123
_jana_atom_site_ADP_E_11133
_jana_atom_site_ADP_E_11222
_jana_atom_site_ADP_E_11223
_jana_atom_site_ADP_E_11233
_jana_atom_site_ADP_E_11333
_jana_atom_site_ADP_E_12222
_jana_atom_site_ADP_E_12223
_jana_atom_site_ADP_E_12233
_jana_atom_site_ADP_E_12333
_jana_atom_site_ADP_E_13333
_jana_atom_site_ADP_E_22222
_jana_atom_site_ADP_E_22223
_jana_atom_site_ADP_E_22233
_jana_atom_site_ADP_E_22333
_jana_atom_site_ADP_E_23333
_jana_atom_site_ADP_E_33333
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

loop_
_jana_atom_site_ADP_F_label
_jana_atom_site_ADP_F_type_symbol
_jana_atom_site_ADP_F_111111
_jana_atom_site_ADP_F_111112
_jana_atom_site_ADP_F_111113
_jana_atom_site_ADP_F_111122
_jana_atom_site_ADP_F_111123
_jana_atom_site_ADP_F_111133
_jana_atom_site_ADP_F_111222
_jana_atom_site_ADP_F_111223
_jana_atom_site_ADP_F_111233
_jana_atom_site_ADP_F_111333
_jana_atom_site_ADP_F_112222
_jana_atom_site_ADP_F_112223
_jana_atom_site_ADP_F_112233
_jana_atom_site_ADP_F_112333
_jana_atom_site_ADP_F_113333
_jana_atom_site_ADP_F_122222
_jana_atom_site_ADP_F_122223
_jana_atom_site_ADP_F_122233
_jana_atom_site_ADP_F_122333
_jana_atom_site_ADP_F_123333
_jana_atom_site_ADP_F_133333
_jana_atom_site_ADP_F_222222
_jana_atom_site_ADP_F_222223
_jana_atom_site_ADP_F_222233
_jana_atom_site_ADP_F_222333
_jana_atom_site_ADP_F_223333
_jana_atom_site_ADP_F_233333
_jana_atom_site_ADP_F_333333
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_squared_calc
_refln_F_squared_meas
_refln_F_squared_sigma
_refln_observed_status
_jana_refln_twin_domain
-1 0 0 33161.30 31541.40 982.51 o -2

CRYSTALS
?

WinGX
Louis Farrugia informs me that he uses no datanames of his own

STOE
?

IUCr
_iucr_refine_instructions_details
_iucr_refine_reflections_details
_iucr_compatibility_tag
_iucr_geom_hbonds_special_details

TWINNING
Victor Young set
(Hopefully, the relevant TWIN/BASF/HKLF5 info can be mapped onto those)
See also the above examples for CrysAlisPro (Agilent) and JANA handling of twins.

PRESSURE of Measurement
Definitions in CIFdic.

FLACK
The various parameter options: Flack-refined, Flack/Parsons (Shelx style),
Parsons, Hooft-Gaussian, Hooft-Student

NEW DATANAMES TO BE DEFINED FOR

1 - Type of experiment (Powder, High Pressure, Incommensurate, charge density)

2 - Institution where the data were collected

3 - The name and contact details (e-mail) of the person who collected the data

4 - The name and contact details of the person submitting the CIF or paper (this might be different from the corresponding author details - we often have the paper/data being submitted by the crystallographer, but the formal corresp. author on the paper is desired to be someone else).

####################################
Chester searched for names appearing in published CIFs

_atom_dummy_fract_x
_atom_dummy_fract_y
_atom_dummy_fract_z
_atom_dummy_label

_atom_site_site_symmetry_mutiplicity (spelling!)


_diffrn_measurement_method_dtprofit.ref

_diffrn_reflns_sin(theta)/lambda_max
_diffrn_reflns_sin(theta)/lambda_min
_diffrn_source_monochromator
!! (should it be _diffrn_radiation_monochromator)

_geom_angle_DHA
_geom_bond_atom_site_label_D
_geom_bond_atom_site_label_H
_geom_bond_distance_DH
_geom_contact_atom_site_label_A
_geom_contact_distance_DA
_geom_contact_distance_HA
_geom_contact_site_symmetry_A

_geom_extra_table_head_A
_geom_extra_table_head_B
_geom_extra_table_head_C
_geom_extra_table_head_D
_geom_extra_table_head_E
_geom_extra_table_head_F
_geom_extra_table_headA
_geom_extra_table_headB
_geom_extra_table_headC
_geom_extra_table_headD
_geom_extra_table_headE
_geom_extra_table_headF
_geom_extra_tableA_col_1
_geom_extra_tableA_col_10
_geom_extra_tableA_col_2
_geom_extra_tableA_col_3
_geom_extra_tableA_col_4
_geom_extra_tableA_col_5
_geom_extra_tableA_col_6
_geom_extra_tableA_col_7
_geom_extra_tableA_col_8
_geom_extra_tableA_col_9
_geom_extra_tableB_col_1
_geom_extra_tableB_col_10
_geom_extra_tableB_col_2
_geom_extra_tableB_col_3
_geom_extra_tableB_col_4
_geom_extra_tableB_col_5
_geom_extra_tableB_col_6
_geom_extra_tableB_col_7
_geom_extra_tableB_col_8
_geom_extra_tableB_col_9
_geom_extra_tableC_col_1
_geom_extra_tableC_col_2
_geom_extra_tableC_col_3
_geom_extra_tableC_col_4
_geom_extra_tableC_col_5
_geom_extra_tableD_col_1
_geom_extra_tableD_col_2
_geom_extra_tableD_col_3
_geom_extra_tableD_col_4
_geom_extra_tableD_col_5
_geom_extra_tableE_col_1
_geom_extra_tableE_col_10
_geom_extra_tableE_col_11
_geom_extra_tableE_col_2
_geom_extra_tableE_col_3
_geom_extra_tableE_col_4
_geom_extra_tableE_col_5
_geom_extra_tableE_col_6
_geom_extra_tableE_col_7
_geom_extra_tableE_col_8
_geom_extra_tableE_col_9
_geom_extra_tableF_col_1
_geom_extra_tableF_col_2
_geom_extra_tableF_col_3
_geom_extra_tableF_col_4
_geom_extra_tableF_col_5
_geom_table_footnote_A
_geom_table_footnote_B
_geom_table_footnote_C
_geom_table_footnote_D
_geom_table_footnote_E
_geom_table_footnote_F
_geom_table_headnote_A
_geom_table_headnote_B
_geom_table_headnote_C



_pd_proc_ls_prof_chi2
_pd_proc_ls_prof_cR_factor
_pd_proc_ls_prof_cwR_expected
_pd_proc_ls_prof_cwR_factor
_pd_proc_ls_prof_echi2


_publ_section_experimental_prep (author mistake? we do not use).
_publ_section_table_captions

_publcif_datablock.id
_publcif_info_datablock.id
_publcif_info_datablock.publ_exptl
_publcif_info_datablock.publ_geom
_publcif_info_datablock.structure
_publcif_info_exptl_table_extra_item
_publcif_info_exptl_table_header_item
_publcif_info_exptl_table_max_cols
_publcif_info_exptl_table_use_headnotes
_publcif_info_tables.block_id
_publcif_info_tables.reference_item
_publcif_jmolscript.caption
_publcif_jmolscript.group
_publcif_jmolscript.id
_publcif_jmolscript.model
_publcif_jmolscript.model_type
_publcif_jmolscript.script
_publcif_jmolscript.type
_publcif_jmolscript.type_group

_refine_diff_density_max/min
_reflns_Friedel_fraction


------------------------------------------------------------------------------
Tony_Linden
 
Posts: 3
Joined: Sat Oct 01, 2011 4:59 pm

Re: Non-defined datnames being used in published CIFs

Postby jamesrhester » Mon Mar 31, 2014 10:39 pm

I agree with the need to keep the definitions usable. I suggest that we start by writing to the program authors requesting a description of the respective datanames. The 'squeeze' datanames might be better developed within this group, and run past the program authors for their comments.
jamesrhester
 
Posts: 39
Joined: Mon Sep 19, 2011 8:21 am


Return to Core CIF review and update

Who is online

Users browsing this forum: No registered users and 0 guests

cron