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draft-diffrn-data-set-example-20170712.cif
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draft-diffrn-data-set-example-20170712.cif
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## File: draft-diffrn-data-set-example-20161005.cif
## Date: 5-Oct-2016
## Updated: 23-Dec-2016 after working group conference call 21-Dec-2016
##
## Example reflection data file following PDBx/mmCIF Deposition Working
## proposal from Sep 19, 2016 Cambridge meeting.
##
## One merged example set, two parent unmerged data sets (w/o real data),
## and one data section that would be included by the PDB archive.
##
## Updated after Dec 21, 2016 conference call
##
data_DIFFRN-PDB_00001ABC
#
# This first data section would be added and maintained by the PDB -
# Accession details
_entry.id 'pdb_00001abc'
#
# Map diffraction id's in the model coordinate file to data sections -
loop_
_pdbx_diffrn_data_section_correspondence.diffrn_id
_pdbx_diffrn_data_section_correspondence.data_section_id
1 'ds-merged-1'
#
loop_
_pdbx_diffrn_data_section_contents.data_section_id
_pdbx_diffrn_data_section_contents.content_type
'ds-merged-1' 'X-ray structure factor amplitudes'
'ds-merged-1' 'X-ray calculated amplitudes'
'ds-merged-1' 'X-ray calculated phases'
'ds-unmerged-1' 'X-ray unmerged intensities'
'ds-unmerged-2' 'X-ray unmerged intensities'
#
# Some audit details -
loop_
_pdbx_data_section_audit.data_section_id
_pdbx_data_section_audit.date
_pdbx_data_section_audit.version
_pdbx_data_section_audit.action_type
'DIFFRN-PDB_00001ABC' 2016-10-01 1.0 'Initial release'
##
# -----------------------------------------------------------------------------------------------
##
data_ds-merged-1
#
# Merged data section -- data_<data_section_id> where data_section_id = 'ds-merged-1'
#
_pdbx_diffrn_data_section.id 'ds-merged-1'
_pdbx_diffrn_data_section.type_scattering 'x-ray'
_pdbx_diffrn_data_section.type_merged 'true'
_pdbx_diffrn_data_section.type_scaled 'true'
_pdbx_diffrn_data_section.details 'Optional details describing this example diffraction data section'
#
# Index of parent data sets contributing to this data section -
#
loop_
_pdbx_diffrn_data_section_index.data_section_id
_pdbx_diffrn_data_section_index.parent_data_section_id
'ds-merged-1' 'ds-unmerged-1'
'ds-merged-1' 'ds-unmerged-2'
#
# Cell constants
#
_pdbx_diffrn_merged_cell.data_section_id 'ds-merged-1'
_pdbx_diffrn_merged_cell.cell_length_a 51.3940
_pdbx_diffrn_merged_cell.cell_length_b 109.0130
_pdbx_diffrn_merged_cell.cell_length_c 137.3070
_pdbx_diffrn_merged_cell.cell_angle_alpha 90.0000
_pdbx_diffrn_merged_cell.cell_angle_beta 90.0000
_pdbx_diffrn_merged_cell.cell_angle_gamma 90.0000
#
# Space group assignment
_pdbx_diffrn_symmetry.data_section_id 'ds-merged-1'
_pdbx_diffrn_symmetry.space_group_name_H-M 'P 21 21 21'
#
#
loop_
_pdbx_diffrn_merge_wavelength_list.id
_pdbx_diffrn_merge_wavelength_list.wavelength
1 0.91837
#
# Statistics for the merged data set -
#
_pdbx_diffrn_merge_stat.data_section_id 'ds-merged-1'
_pdbx_diffrn_merge_stat.d_resolution_high 1.32
_pdbx_diffrn_merge_stat.d_resolution_low 150.0
_pdbx_diffrn_merge_stat.number_obs 300000
_pdbx_diffrn_merge_stat.number_all 308123
_pdbx_diffrn_merge_stat.mean_I_over_sigI_all 10.7
_pdbx_diffrn_merge_stat.Rmerge_all 0.069
_pdbx_diffrn_merge_stat.Rpim_I_all 0.033
_pdbx_diffrn_merge_stat.CC_half_all 0.999
_pdbx_diffrn_merge_stat.percent_possible_obs 98.2
# Merged reflection list -
#
# loop _
# <reflection id> <h-asu> <k-asu> <l-asu> <status> <r_free_flag> ...
#
# with
# <I> <sigI> <<< F_meas_au, F_meas_sigma_au
# <F> <sigF> <<< I_meas_au, I_meas_sigma_au
#
loop_
_pdbx_diffrn_merged_refln.reflection_id
_pdbx_diffrn_merged_refln.index_h
_pdbx_diffrn_merged_refln.index_k
_pdbx_diffrn_merged_refln.index_l
_pdbx_diffrn_merged_refln.F_meas_au
_pdbx_diffrn_merged_refln.F_meas_sigma_au
_pdbx_diffrn_merged_refln.F_calc_au
_pdbx_diffrn_merged_refln.phase_calc
_pdbx_diffrn_merged_refln.status
_pdbx_diffrn_merged_refln.R_free_flag
1 0 0 8 918.100 7.0000 2128.50 0.0000 o 1
2 0 0 10 450.700 5.3000 787.600 180.000 o 1
3 0 0 12 875.000 7.1000 851.000 180.000 o 10
4 0 0 14 628.700 6.4000 468.400 180.000 o 10
5 0 0 18 492.000 7.3000 565.200 180.000 o 5
# ... abbreviated ...
##
#
# Merged data set - crystals contributing to this merged data set -
#
loop_
_pdbx_diffrn_merge_crystal_list.data_section_id
_pdbx_diffrn_merge_crystal_list.crystal_id
'ds-unmerged-1' 1
'ds-unmerged-2' 1
#
#
# Merged data set - image and crystal mapping list -
#
loop_
_pdbx_diffrn_merge_image_list.data_section_id
_pdbx_diffrn_merge_image_list.crystal_id
_pdbx_diffrn_merge_image_list.image_id
'ds-unmerged-1' 1 1
'ds-unmerged-1' 1 2
'ds-unmerged-2' 1 1
'ds-unmerged-2' 1 2
#
# Merged data set - rejected reflection list
loop_
_pdbx_diffrn_merge_rejected_list.data_section_id
_pdbx_diffrn_merge_rejected_list.reflection_id
_pdbx_diffrn_merge_rejected_list.image_id
'ds-unmerged-1' 1 1
'ds-unmerged-1' 2 1
'ds-unmerged-2' 5 1
# -----------------------------------------------------------------------------------------------
##
data_ds-unmerged-1
#
# Unmerged data section #1 -- data_<data_section_id> where data_section_id = 'ds-unmerged-1'
#
_pdbx_diffrn_data_section.id 'ds-unmerged-1'
_pdbx_diffrn_data_section.type_scattering x-ray
_pdbx_diffrn_data_section.type_merged false
_pdbx_diffrn_data_section.type_scaled true
_pdbx_diffrn_data_section.details 'Optional details describing this example diffraction data section'
#
# Facility/beamline proposal tracking details
#
_pdbx_diffrn_data_section_experiment.ordinal 1
_pdbx_diffrn_data_section_experiment.data_section_id 'ds-unmerged-1'
_pdbx_diffrn_data_section_experiment.proposal_id 1234A
#
# Facility/beamline details for this data collection
#
_pdbx_diffrn_data_section_site.data_section_id 'ds-unmerged-1'
_pdbx_diffrn_data_section_site.facility APS
_pdbx_diffrn_data_section_site.beamline 14-BM-C
_pdbx_diffrn_data_section_site.collection_date 2016-09-11
_pdbx_diffrn_data_section_site.detector 'ADSC QUANTUM 315'
_pdbx_diffrn_data_section_site.detector_type CCD
#
# List of crystal samples in this data set
#
loop_
_pdbx_diffrn_unmerged_cell.ordinal
_pdbx_diffrn_unmerged_cell.crystal_id
_pdbx_diffrn_unmerged_cell.wavelength
_pdbx_diffrn_unmerged_cell.cell_length_a
_pdbx_diffrn_unmerged_cell.cell_length_b
_pdbx_diffrn_unmerged_cell.cell_length_c
_pdbx_diffrn_unmerged_cell.cell_angle_alpha
_pdbx_diffrn_unmerged_cell.cell_angle_beta
_pdbx_diffrn_unmerged_cell.cell_angle_gamma
1 1 .91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
2 2 .91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
# ... abbreviated ...
#
# List of image processing details for each crystal
#
# loop_
# <image id> <image number> <crystal id> <a> <b> <c> <alpha> <beta> <gamma> <wavelength> <phi-image>
#
#
loop_
_pdbx_diffrn_image_proc.image_id
_pdbx_diffrn_image_proc.crystal_id
_pdbx_diffrn_image_proc.image_number
_pdbx_diffrn_image_proc.phi_value
_pdbx_diffrn_image_proc.wavelength
_pdbx_diffrn_image_proc.cell_length_a
_pdbx_diffrn_image_proc.cell_length_b
_pdbx_diffrn_image_proc.cell_length_c
_pdbx_diffrn_image_proc.cell_angle_alpha
_pdbx_diffrn_image_proc.cell_angle_beta
_pdbx_diffrn_image_proc.cell_angle_gamma
1 1 1 0.5000 0.91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
1 2 1 0.6000 0.91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
# .... abbreviated ...
#
# Unmerged intensity reflection list
#
# loop_
# <reflection id> <image id start> <image id end> <h-original> <k-original> <l-original> <phi-reflection> <partiality>
#
# with
# <I> <sigI> <<< intensity_meas, intensity_sigma
# <I-sum> <sigI-sum> <<< intensity_sum, intensity_sum_sigma
# <I-profile> <sigI-profile> <<< intensity_profile, intensity_profile_sigma
#
#
loop_
_pdbx_diffrn_unmerged_refln.reflection_id
_pdbx_diffrn_unmerged_refln.image_id_begin
_pdbx_diffrn_unmerged_refln.image_id_end
_pdbx_diffrn_unmerged_refln.index_h
_pdbx_diffrn_unmerged_refln.index_k
_pdbx_diffrn_unmerged_refln.index_l
_pdbx_diffrn_unmerged_refln.intensity_meas
_pdbx_diffrn_unmerged_refln.intensity_sigma
_pdbx_diffrn_unmerged_refln.phi_reflection
_pdbx_diffrn_unmerged_refln.partiality
1 1 1 0 0 5 28.800 264.700 .500 1.0
# ... abbreviated ...
# -----------------------------------------------------------------------------------------------
##
##
data_ds-unmerged-2
#
# Unmerged data section #2 -- data_<data_section_id> where data_section_id = 'ds-unmerged-2'
#
_pdbx_diffrn_data_section.id 'ds-unmerged-2'
_pdbx_diffrn_data_section.type_scattering x-ray
_pdbx_diffrn_data_section.type_merged false
_pdbx_diffrn_data_section.type_scaled true
_pdbx_diffrn_data_section.details 'Optional details describing this example diffraction data section'
#
# Facility/beamline proposal tracking details
#
_pdbx_diffrn_data_section_experiment.ordinal 1
_pdbx_diffrn_data_section_experiment.data_section_id 'ds-unmerged-2'
_pdbx_diffrn_data_section_experiment.proposal_id 1234A
#
# Facility/beamline details for this data collection
#
_pdbx_diffrn_data_section_site.data_section_id 'ds-unmerged-2'
_pdbx_diffrn_data_section_site.facility APS
_pdbx_diffrn_data_section_site.beamline 14-BM-C
_pdbx_diffrn_data_section_site.collection_date 2016-09-12
_pdbx_diffrn_data_section_site.detector 'ADSC QUANTUM 315'
_pdbx_diffrn_data_section_site.detector_type CCD
#
# List of crystal samples in this data set
#
loop_
_pdbx_diffrn_unmerged_cell.ordinal
_pdbx_diffrn_unmerged_cell.crystal_id
_pdbx_diffrn_unmerged_cell.wavelength
_pdbx_diffrn_unmerged_cell.cell_length_a
_pdbx_diffrn_unmerged_cell.cell_length_b
_pdbx_diffrn_unmerged_cell.cell_length_c
_pdbx_diffrn_unmerged_cell.cell_angle_alpha
_pdbx_diffrn_unmerged_cell.cell_angle_beta
_pdbx_diffrn_unmerged_cell.cell_angle_gamma
1 1 .91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
2 2 .91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
# ... abbreviated ...
#
# List of image processing details for each crystal
#
# loop_
# <image id> <image number> <crystal id> <a> <b> <c> <alpha> <beta> <gamma> <wavelength> <phi-image>
#
loop_
_pdbx_diffrn_image_proc.image_id
_pdbx_diffrn_image_proc.crystal_id
_pdbx_diffrn_image_proc.image_number
_pdbx_diffrn_image_proc.phi_value
_pdbx_diffrn_image_proc.wavelength
_pdbx_diffrn_image_proc.cell_length_a
_pdbx_diffrn_image_proc.cell_length_b
_pdbx_diffrn_image_proc.cell_length_c
_pdbx_diffrn_image_proc.cell_angle_alpha
_pdbx_diffrn_image_proc.cell_angle_beta
_pdbx_diffrn_image_proc.cell_angle_gamma
1 1 1 0.5000 0.91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
1 2 1 0.6000 0.91837 51.3940 109.0130 137.3070 90.000 90.000 90.000
# .... abbreviated ...
#
# Unmerged intensity reflection list
#
# loop_
# <reflection id> <image id start> <image id end> <h-original> <k-original> <l-original> <phi-reflection> <partiality>
#
# with
# <I> <sigI> <<< intensity_meas, intensity_sigma
# <I-sum> <sigI-sum> <<< intensity_sum, intensity_sum_sigma
# <I-profile> <sigI-profile> <<< intensity_profile, intensity_profile_sigma
#
loop_
_pdbx_diffrn_unmerged_refln.reflection_id
_pdbx_diffrn_unmerged_refln.image_id_begin
_pdbx_diffrn_unmerged_refln.image_id_end
_pdbx_diffrn_unmerged_refln.index_h
_pdbx_diffrn_unmerged_refln.index_k
_pdbx_diffrn_unmerged_refln.index_l
_pdbx_diffrn_unmerged_refln.intensity_meas
_pdbx_diffrn_unmerged_refln.intensity_sigma
_pdbx_diffrn_unmerged_refln.phi_reflection
_pdbx_diffrn_unmerged_refln.partiality
1 1 1 0 0 5 28.800 264.700 .500 1.0
# ... abbreviated ...
# -----------------------------------------------------------------------------------------------