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Macromolecular dictionary (mmCIF) version 2.0.09
Revision history
========================================================================
Version 0.1.1 (1993-02-11)
------------------------------------------------------------------------
Highlighted all notes with # %%%%% surrounds.
========================================================================
Version 0.1.2 (1993-02-11)
------------------------------------------------------------------------
Started moving examples to *_appendix data items.
========================================================================
Version 0.1.3 (1993-02-11)
------------------------------------------------------------------------
Started moving core data names to the *_appendix data items
========================================================================
Version 0.1.4 (1993-02-11)
------------------------------------------------------------------------
Added example for _symmetry_
========================================================================
Version 0.1.5 (1993-03-24)
------------------------------------------------------------------------
Finished moving examples to *_appendix data items
========================================================================
Version 0.1.6 (1993-03-24)
------------------------------------------------------------------------
Dealt with many issues raised by SR Hall.
Some were merely typographical.
Changed temp to B_iso
Changed occ to occupancy
Changed special_details to details.
Changed asl to label everywhere.
Shuffled data names in _struct_conf_ and _struct_conn_
========================================================================
Version 0.1.7 (1993-03-24)
------------------------------------------------------------------------
Tested for Cyclops compliance - most problems are names that
are too long.
Changed crystal_preparation to crystal_prep
Changed d_resolution to d_res
Many other such changes
========================================================================
Version 0.1.8 (1993-03-25)
------------------------------------------------------------------------
Still testing for Cyclops compliance - reveal many additional
syntax problems
Also verified with new tool by RG Ball - still more errors fixed
Dealt with issue raised by PE Bourne - amongst changes
Rewrote _database_ section completely
Changed _audit_contact_author_ to
_audit_contact_author_name
_audit_contact_author_address
========================================================================
Version 0.1.9 (1993-03-26)
------------------------------------------------------------------------
Removed _struct_topol_ section until it gets straightened out
========================================================================
Version 0.1.10 (1993-03-28)
------------------------------------------------------------------------
Filled in examples for several data categories
========================================================================
Version 0.1.11 (1993-04-03)
------------------------------------------------------------------------
Syntax checked using tools of Peter Murray-Rust - many problems fixed
========================================================================
Version 0.1.12 (1993-04-06)
------------------------------------------------------------------------
More syntax problems fixed a la Peter Murray-Rust
========================================================================
Version 0.1.13 (1993-04-07)
------------------------------------------------------------------------
Introduced _exptl_crystal_grow_ data names
========================================================================
Version 0.1.14 (1993-04-07)
------------------------------------------------------------------------
Experiment with refers_to, category and part_of_key in
entity_conn_atom_ and entity_conn_bond_ sections.
Discovered horror show with nonconcurrent versions on different
computers - not yet resolved.
========================================================================
Version 0.1.15 (1993-05-09)
------------------------------------------------------------------------
Reconciled nonconcurrent versions
Removed trailing blanks
Made corrections based on email suggestions from P. Bourne
========================================================================
Version 0.1.16 (1993-05-10)
------------------------------------------------------------------------
Made corrections based on written comments from K. Watenpaugh
Made corrections/additions based on discussions at Rutgers
========================================================================
Version 0.1.17 (1993-05-11)
------------------------------------------------------------------------
Changed _atom_site_label_component_? to new nomenclature
Introduced category DDL throughout
Introduced refers_to DDL throughout
Introduced part_of_key DDL throughout
Mandated that _list must be in each data definition
Standardized 'need not be unique' statements
Standardized example headers
========================================================================
Version 1.1.18 (1993-05-12)
------------------------------------------------------------------------
Looped out authors and editors in citation list
Verified with RGB tools
Some style consistency imposed
Fleshed out category definitions and imposed style
Updated "sets of data item" at beginning of document
Checked alphabetical order of data names - moved id's
========================================================================
Version 0.2.1 (1993-05-13)
------------------------------------------------------------------------
Major rethinking of _entity_ data based following discussions
of 1993-05-10 meeting
========================================================================
Version 0.2.2 (1993-05-18)
------------------------------------------------------------------------
Style consistency and proof reading changes throughout
Make page numbers general to articles and chapters in citation
Added *_method to all phasing categories
Looped out keywords from _struct_site_ list
Added _atom_site_label_ definitions as per H. Berman
Added _struct_biol_view_ and struct_site_view_ items as per P. Bourne
Added _atom_sites_alt_ data items to formally handle alternative
conformations
Verified with Cyclops and RGB tools
========================================================================
Version 0.2.3 (1993-05-19)
------------------------------------------------------------------------
Fixed based on problems unearthed by Peter Murray-Rust and Brian McMahon
========================================================================
Version 0.2.4 (1993-05-20)
------------------------------------------------------------------------
DDL adjustment from down under ):-(>
========================================================================
Version 0.2.5 (1993-05-20)
------------------------------------------------------------------------
A general merging of updates from PMR, BMcM and SRH
Fixed typographical and stylistic problems a la BMcM
========================================================================
Version 0.2.6 (1993-06-02)
------------------------------------------------------------------------
Fixed _atom_site_ example (_entity_poly_seq_num)
Removed _list_link_parent from _entity_mon_atom_atom_id a
_entity_nonp_atom_atom_id
Added real APS coordinates to _atom_site_ example
Rewrote _atom_sites_footnote_ example
========================================================================
Version 0.2.7 (1993-08-01)
------------------------------------------------------------------------
Redesigned phasing_MIR definitions
========================================================================
Version 0.2.8 (1993-08-03)
------------------------------------------------------------------------
More work on phasing_MIR
Created phasing_MIR_der and phasing_MIR_der_shell categories
========================================================================
Version 0.3.1 (1993-08-08)
------------------------------------------------------------------------
Began implementing DDL v0.7
========================================================================
Version 0.3.2 (1993-08-11)
------------------------------------------------------------------------
Cleaning up of stray notes
========================================================================
Version 0.3.3 (1993-08-12)
------------------------------------------------------------------------
Syntax and consistency checks - SRH
Added _type of null for appendix items.
========================================================================
Version 0.3.4 (1993-09-01)
------------------------------------------------------------------------
Added _struct_conn_ptnr1_label_alt_id and
_struct_conn_ptnr2_label_alt_id
Corrected definitions for _struct_conn_ptnr2_ items
Added _struct_site_gen_label_alt_id
Fixed Cullis reference in _phasing_MIR_der_shell_R_Cullis
Change _database_PDB_rev_ example to _loop construction
Added _PDB_remark category (data items _PDB_remark_num and
_PDB_remark_text)
Added 'obsolete' to enumeration list for _database_PDB_rev_status
Added _database_PDB_rev_replaces data item
========================================================================
Version 0.3.5 (1993-09-08)
------------------------------------------------------------------------
Added missing _diffrn_orient_matrix_UB_33 (in appendix)
Added missing _phasing_MIR_der_shell_der_id to appropriate example
========================================================================
Version 0.3.6 (1993-10-10)
------------------------------------------------------------------------
Changed *_appendix to *_[mm] throughout
Removed 'Need example here' from _chemical_[mm]
Removed 'Need example here' from _chemical_conn_atom_[mm]
Removed 'Need example here' from _chemical_conn_bond_[mm]
Moved _PDB to end of all relevant data names (except _[mm])
Added _database_rev_record_details_PDB data name
Changed _refine_occupancy_limit_high to _refine_occupancy_max
Changed _refine_occupancy_limit_low to _refine_occupancy_min
Changed _refine_B_iso_limit_high to _refine_B_iso_max
Changed _refine_B_iso_limit_low to _refine_B_iso_min
Changed all definitions and examples in _refine_iso_B_ category
to _refine_B_iso_ equivalents
========================================================================
Version 0.3.7 (1993-11-16)
------------------------------------------------------------------------
Changed form of dates in _update_history to CIF style
Changed ? to . in examples, where appropriate
Added _example_detail to _refine_ls_restr_type
Expanded definition of _refine_ls_restr_type
========================================================================
Version 0.3.8 (1993-11-30)
------------------------------------------------------------------------
Moved _audit_author_, _citation_ categories to CIF core
Definitions and small-molecule examples removed from *_[mm]
sections that don't extend core categories - BMcM
========================================================================
Version 0.3.9 (1993-12-02)
------------------------------------------------------------------------
Deleted section summarizing categories - PMDF
Returned definitions for most *_[mm] sections - PMDF
Added _list and _list_level to global - PMDF
Changed form of dates from yy-mm-dd to yyyy-mm-dd - PMDF
Checked lists of data items in core, fixing some problems
with missing names and alphabetization - PMDF
Resorted some categories to correct alphabetization - PMDF
Changed form and definitions of _database_remark_num_PDB and
_database_remark_text_PDB - PMDF
Added data item _database_rev_replaced_by_PDB - PMDF
Reordered data items in _citation example - PMDF
Added data item _exptl_crystal_density_%_sol - PMDF
========================================================================
Version 0.3.10 (1993-12-15)
------------------------------------------------------------------------
Various changes following suggestions from BMcM
Refined definition of _atoms_site_label_atom_id - PMDF
Removed _atom_sites_fract_tran (moved to core) - PMDF
Changed _diffrn_crystal_physical_device to
_diffrn_crystal_support - PMDF
Changed _diffrn_measure_device_part to
_diffrn_measure_device_specific - PMDF
Changed _diffrn_rad_detector_part to
_diffrn_rad_detector_specific - PMDF
Changed _diffrn_rad_source_part to
_diffrn_rad_source_specific - PMDF
Changed *_par1* and *_par2* to *_ptnr* in _struct_conn* - PMDF
Fixed several occurrences of \&A instead of \%A - PMDF
========================================================================
Version 0.3.11 (1993-12-22)
------------------------------------------------------------------------
Made a number of fixes relayed by PEB from MS AND RH
_type of _atom_site_footnote_id (numb->char) - PMDF
_type of _database_rev_record_rev_num_PDB (char->numb) - PMDF
_type of _phasing_MIR_der_number_of_sites (char->numb) - PMDF
_atom_sites_fract_tran_matrx to _matrix - PMDF
_type of _phasing_MIR_site_details (numb->char) - PMDF
_example of _struct_conf_type_reference - PMDF
========================================================================
Version 0.3.12 (1993-12-23)
------------------------------------------------------------------------
Broke out examples from intro sections to loop_ _item_examples.case
_example_detail construction - BMcM
========================================================================
Version 0.3.13 (1994-01-13)
------------------------------------------------------------------------
Rationalization of categories between mm and core dicts - BMcM
Deleted _diffrn_crystal_environment (same as core
_diffrn_ambient_environment) and moved other _diffrn_crystal
items to core - BMcM
Fixed typos, removed hyphenation ("be kind to ciftex") - BMcM
Some re-alphabetization - BMcM
========================================================================
Version 0.3.14 (1994-01-26)
------------------------------------------------------------------------
Lots more re-alphabetization - PMDF
Changed non_s to nstd throughout - PMDF
Changed nonp to npol throughout - PMDF
Removed all multiple spaces - PMDF
Fixed a couple of alignment problems - PMDF
========================================================================
Version 0.4.1 (1994-02-04)
------------------------------------------------------------------------
Major modifications of _entity_ subcategories - PMDF
Added angles, planes, torsion angles and chiral centers to
_entity_mon_ and _entity_npol_
Added many missing definitions
Added many missing examples
========================================================================
Version 0.4.2 (1994-02-25)
------------------------------------------------------------------------
Corrected spelling errors found by BMcM - PMDF
========================================================================
Version 0.4.3 (1994-03-28)
------------------------------------------------------------------------
Various changes following suggestions by IDB - PMDF
Changed _entity_mon_angle_value to
_entity_mon_angle_value_angle in example
Changed _entity_npol_bond_value to
_entity_npol_bond_value_dist
Changed nonp to npol in _entity_npol_tor_value category
Reworded angle _enumeration_details in _refine_ls_restr_type
Reworded definitions in _struct_asym_[mm] and _struct_biol_[mm]
Reworded definitions of _struct_conn_symmetry_*
_struct_site_gen_symmetry
_struct_biol_gen_symmetry
Split _struct_conn_symmetry_* into
_struct_conn_ptnr1_symmetry and
_struct_conn_ptnr2_symmetry
Split _struct_conn_role_* into
_struct_conn_ptnr1_role and
_struct_conn_ptnr2_role
Removed _list_link_child from _struct_conn_conn_type_id
Added _list_link_child to _struct_conn_type_id
========================================================================
Version 0.5.1 (1994-10-10)
------------------------------------------------------------------------
Implementation of Treaty of Brussels - PMDF
Merged CIF core dated 1994-03-01 (from BMcM) with mm dictionary
dated 1994-05-20.
The history records for the core dictionary are included here
to identify the version of the core that was merged:
_dictionary_name cifdic.c94
_dictionary_version 2.0
_dictionary_update 1994-03-01
_dictionary_history
1991-05-27 Created from CIF Dictionary text. SRH
1991-05-30 Validated with CYCLOPS & CIF ms. SRH
1991-06-03 Adjustments to some definitions. SRH
1991-06-06 Adjustments a la B. McMahon. SRH
1991-06-18 Additions & some redefinitions. SRH
1991-07-04 Corrected 90:0 in *_detect_slit_. SRH
1991-09-20 Additions & some redefinitions. SRH
1991-09-20 Final published version. IUCr
1991-11-12 Add _diffrn_ambient_environment. SRH
1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH
1993-02-23 Apply global_ and 'unknown' -> '?' SRH
1993-03-05 Changes resulting from MM dictionary. SRH
1993-05-20 Changes arising from new DDL commands. SRH
1993-08-05 Additional fine tuning pre-Beijing. SRH
1993-12-22 Introductory sections added to categories. BMcM
1993-12-22 Additional categories from mm work: _audit_author,
_citation, _atom_sites_fract_tran_matrix. BMcM
1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM
1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM
1994-03-01 Add 'atom_site_aniso_ratio'. BMcM
--------------
Removed all mm sections that enumeration items present in core
but not present in mm dictionary.
Fixed errors with missing trailing _'s in some category headers
Also unbalanced ##'s in same place
Removed "End of Example" statement everywhere
Standardized syntax for missing examples
Standardized syntax and style for category _definition data
items. Added a bunch of ending dashed lines where they were missing.
<Saved Brussels_airplane_1 at this point and began new file.>
Merged [] and [mm] category explanation sections. Made HIV
example always example 1, moved examples from core (where
they were different from the HIV example) to higher numbers.
<Saved Bussels_airplane_2 at this point - [] and [mm] sections
not yet completely merged..
========================================================================
Version 0.5.2 (1994-11-09)
------------------------------------------------------------------------
Implementation of DDL 2.0.7 in CITATION category - PMDF & JW
========================================================================
Version 0.5.3 (1994-11-13)
------------------------------------------------------------------------
Implementation of DDL 2.0.7 dictionary wide - PMDF
Finished merging [] and [mm] sections
<Saved newddl_all_1 at this point>
Changed data_ to save_ everywhere
Changed _name to _item.name everywhere
Added _item.mandatory_code everywhere
Added save_ everywhere
Moved _description to top of _save frame everywhere
Changed _example to _item_examples.case everywhere
Changed _example_detail to _item_examples.detail everywhere
Changed _description to _item.description.description
everywhere
Removed _list yes everywhere
Removed _list_reference everywhere
Changed _enumeration_range to enumeration_limit.minimum and
enumeration_limit.maximum everywhere
<saved newddl_all_2 at this point>
========================================================================
Version 0.5.4 (1994-11-14)
------------------------------------------------------------------------
Implementation of DDL 2.0.7 dictionary wide - PMDF
Changed _enumeration to _enumeration.code
Changed _enumeration_detail to _enumeration.code_detail
Changed _enumeration_default to _enumeration_default.code
Put .'s in item names (incomplete)
Moved _PDB back to appropriate place in item names in the
_database_remark_PDB_ and _database_rev_PDB_ and
_database_rev_record_PDB_ categories
Changed database_rev_PDB to database_PDB_rev
Changed database_remark_PDB to database_PDB_remark
Changed database_rev_record_PDB to database_PDB_rev_record
Changed category items from item to category
Began getting rid of *_whatever construction in category
and item descriptions
<saved newddl_all_3 at this point>
========================================================================
Version 0.5.5 (1994-11-15)
------------------------------------------------------------------------
Implementation of DDL 2.0.7 dictionary wide - PMDF
Finished putting .'s in itme names
Changed _diffrn_measure_ to _diffrn_measurement.
Changed _diffrn_rad_ to _diffrn_radiation.
<saved newddl_all_4 at this point>
Implemented category and ID pointers for entity category.
Found all sorts of errors while doing this, and attempted
to fix them consistently. Did not remove child data
Items, even though they don't have to be specified - they
should help keep all of this straight during the transition.
Some silly reformatting to ensure that data values always
have the first alphabetic character in column 33.
More silly reformatting to put each example in an example
loop on a separate line.
<saved newddl_all_4 at this point and sent copy to JW>
========================================================================
Version 0.6.1 (1994-11-21)
------------------------------------------------------------------------
Changes (JDW):
+ Converted dictionary and dictionary_history categories.
Incorporated core dictionary history list into the new
history list in the revision 0.5.1 where the dictionary
merger is firsted discussed.
========================================================================
Version 0.6.2 (1994-11-28)
------------------------------------------------------------------------
Changes (PMDF):
+ Made loop_ _item.name data items into separate data items
This involved rewriting the definitions of most of them.
In doing so I continued to eliminate the a.b_* construction.
Added unit type of degrees.
Added unit type of minutes.
Added unit type of electrons.
========================================================================
Version 0.6.3 (1994-11-30)
------------------------------------------------------------------------
Changes (PMDF):
+ Finished conversion of units data items
Added a number of unit types to the table
Conversation table still need to be fleshed out
Removed _list_mandatory and changed _item_mandatory.code to yes for
those data items
========================================================================
Version 0.6.4 (1994-12-01)
------------------------------------------------------------------------
Changes (PMDF):
+ Began conversion of _list_link_parent items to appropriate new DDL
relationships
========================================================================
Version 0.6.5 (1994-12-02)
------------------------------------------------------------------------
Changes (PMDF):
+ Began implementation of new scheme for relationships in the entity
category
All entities will be treated as polymers - non-polymers will have
a number of monomers of 1
All data items in ENTITY_NPOL categories are eliminated
All data items in ENTITY_POLY category are moved to ENTITY
========================================================================
Version 0.6.6 (1994-12-06)
------------------------------------------------------------------------
Changes (PMDF):
+ Finished conversion of _list_link_parent items to appropriate new DDL
relationships
Filled out category_key.id items in each category
Had to add diffrn_refln.id item, as cannot use h k l in that category
(perfectly valid to measure same reflection more than once).
Used _diffrn_standard_refln.code in that category - this may cause a
problem with old files, as example file did not give this data item
Moved _entity_poly items back to _entity category
Moved _entity_poly.formula_weight to entity.formula_weight
Used _exptl_crystal.id in that category - this may cause a
problem with old files, as example file did not give this data item
Added _exptl_crystal_grow.crystal_id in that category
Added _symmetry_equiv.id in that category - this may cause a
problem with old files, as this is a new data item
========================================================================
Version 0.6.7 (1994-12-07)
------------------------------------------------------------------------
Changes (PMDF):
+ Created DATABASE_NEW category to solve logical problems with old DATABASE
category. Need to think some more about how old data items are handled.
Added aliases for remaining c91 data items
Changed geom_angle to geom_angle.value (aliased to original name)
Changed geom_torsion to geom_torsion.value (aliased to original name)
Returned ATOM_SITE items taken out during ATOM_SITE_MM transition
========================================================================
Version 0.6.8 (1994-12-08)
------------------------------------------------------------------------
Changes (PMDF):
+ Created ATOM_SITE_ANISOTROP category to provide for ability to have
anisotropic data is a separate loop, if desired.
Checked and fixed a bunch of style things
Added item_units.code of degrees in data items with degrees in the
description but not in the ddl
Added item_units.code of kelvin in data items with kelvin in the
description but not in the ddl (and added 'in degrees kelvin' to the
description of those with item_units.code of kelvin but no corresponding
phrase in the description)
Added item_units.code of microseconds to _diffrn_radiation.detector_dtime
(added to units list at same time)
Added 'in minutes' to description of _diffrn_refln.elapsed_time
Added 'in kilopascals' to to the description of those with item_units.code
of kilopascals but no corresponding phrase in the description
Added BLOCK category
Added appropriate pointers (in category key, and with a data item
pointing to _data_block.id) in all categories that needed them
========================================================================
Version 0.6.9 (1994-12-09)
------------------------------------------------------------------------
Changes (PMDF):
+ Added _esd data items where needed
Rationalized descriptions for all of the coordinate data items
========================================================================
Version 0.6.10 (1994-12-13)
------------------------------------------------------------------------
Changes (PMDF):
+ Established check-list for unfinished tasks and began dealing with them
Added enumeration limits of 0 and 1 and enumeration default of 1.0 to
occupancy data items
Left heavy-atom maximum with an enumeration of ?
Added enumeration default of 1_555 to all _symmetry data items where it was
missing
Changed 'connect type' to 'interaction' in _struct_conn_type data items.
Filled out sub_category ddl items for cartesian coordinates, fractional
coordinates, cartesian coordinates esds, and Miller indices.
========================================================================
Version 0.6.11 (1994-12-14)
------------------------------------------------------------------------
Changes (PMDF):
+ Fixed R-Kraut reference
Changed _reflns_shell.possible_&_all to _reflns_shell.percent_possible_all
Changed _reflns_shell.possible_&_obs to _reflns_shell.percent_possible_obs
Changed _exptl_crystal.density_%_sol to _exptl_crystal.density_percent_sol
Included full formula for this calculation in description
Changed _refine_ls_restr.model _refine_ls_restr.dev_ideal
Changed _refine_ls_restr.target _refine_ls_restr.dev_ideal_target
Improved wording of all definitions in REFINE_LS_RESTR
Explained sums in _reflns_shell.Rmerge_I_obs and related data items
========================================================================
Version 0.6.12 (1994-12-15)
------------------------------------------------------------------------
Changes (PMDF):
+ Changed _enumeration_default.code to _item_default.value
Changed _enumeration_default.value to _item_default.value
Changed _enumeration.code to _item_enumeration.value
Changed _enumeration.detail to _item_enumeration.detail
Changed _enumeration.case to _item_enumeration.value
Changed _enumeration_limit.maximum to _item_range.maximum
Changed _enumeration_limit.minimum to _item_range.minimum
Checked that matrix were properly labeled as either rw_rowwise or just
plan rowwise.
Reworded matrix descriptions for consistency.
Got rid of the last of the a.b_* constructions in descriptions
Added cell_length, cell_length_esd, cell_angle and cell_angle_esd
subcategories
Changed special_details to details for core items - original names retained
in aliases
Added atom_site.id
Added mm_atom_site_label subcategory
Commented out _atom_site.label_component until it can be dealt with
properly
Changed 'SIF' to 'data block' in a number of descriptions.
========================================================================
Version 0.6.13 (1994-12-16)
------------------------------------------------------------------------
Changes (PMDF):
+ Added data item _refln.R_free_status
Added data item _reflns.R_free_details
Changed _refine_ls_shell.reflns to refine_ls_shell.number_obs
Added _refine_ls_shell.number_R_free
Added _refine_ls_shell.number_all
Added _refine_ls_shell.R_factor_R_free
Added _refine_ls_shell.wR_factor_R_free
Tidied up the count and R-factor descriptions in REFINE_LS_SHELL
Added appropriate item_related names to the R-factors in REFINE_LS_SHELL
Changed 'count' to 'number' in several data names
Changed _reflns.number_total to _reflns.number_all
Changed _reflns.number_observed to _reflns.number.obs
Added _refine.ls_R_factor_R_free
Added _refine.ls_wR_factor_R_free
Edited descriptions of the other R-factor data items in the REFINE
category to conform to the style in REFINE_LS_SHELL
Re-alphabetized the things I changed yesterday from special_details to
details - I had forgotten to do that yesterday
========================================================================
Version 0.6.14 (1994-12-19)
------------------------------------------------------------------------
Changes (PMDF):
+ Changed refine.ls_number_reflns to refine.ls_number_reflns_obs
Added refine.ls_number_reflns_all
Added refine.ls_number_reflns_R_free
Changed _refln.observed_status to refln.status
Expanded enumeration list to include resolution limits and R-free flag
Rewrote definition
Eliminated refln.R_free_status
Changed _refine_ls_shell.number_all to _refine_ls_shell.number_reflns_all
Changed _refine_ls_shell.number_obs to _refine_ls_shell.number_reflns_obs
Changed _refine_ls_shell.number_R_free to
_refine_ls_shell.number_reflns_R_free
Added PHASING category
Filled in and reformatted units conversion table
========================================================================
Version 0.7.1 (1994-12-19)
------------------------------------------------------------------------
Changes (JDW):
+ First pass through SIFLIB checking tools. Corrected syntax errors and
missing parent references.
========================================================================
Version 0.7.2 (1994-12-20)
------------------------------------------------------------------------
Changes (PMDF):
+ Merged JDW changes with version 0.6.12
Changed _item_type.code of numb to either int or float
Changed _item_description.description to category.description where
appropriate
Fixed a bunch of pure syntax errors
Removed 'refln_scale_group' from list of category groups.
Changed _refln_scale_group_code to _refln.scale_group_code somewhere
Changed REFLN_SCALE_GROUP_CODE to _refln.scale_group_code somewhere
Reformatted CATEGORY_GROUP_LIST items to match style of other
header categories
Ensures that all _category data items obey they rule of first
alphabetic character is column 34 (most didn't before this check)
Removed _item_related stuff from _atom_site.aniso_U[1][1] (at the
rest) data items, and added wording to description that these
items are only there for compliance via the alias (but left in
the one _item_related thing that made the matrix element data item
alternate exclusive to the full matrix data item
Added language about compliance to _atom_sites.Cartn_tran_matrix
Added language about compliance to _diffrn_orient_matrix.UB
Added language about compliance to _diffrn_reflns.transf_matrix
Removed matrix element data items for _atom_sites.fract_tran_matrix -
this wasn't in c91 and so doesn't need aliasing
========================================================================
Version 0.7.3 (1994-12-22)
------------------------------------------------------------------------
Changes (PMDF):
+ Fixed things turned up by JDW checking of 0.7.2
Couple of small typos
Added angstroms_cubed to units list and conversion tables
Added _phasing_MIR_site.atom_type_symbol and added this reference to the
table until _atom_type.symbol
Added _entity_mon_atom.substruct_code
Began adding STRUCT_MON_PROT, but this is not yet complete
========================================================================
Version 0.7.4 (1995-01-12)
------------------------------------------------------------------------
Changes (PMDF):
+ Finished working on STRUCT_MON_PROT category
Added STRUCT_MON_DETAILS category
Added STRUCT_MON_PROT_CIS category
Added STRUCT_NCS_ENS category
Added STRUCT_NCS_ENS_OPER category
Added STRUCT_NCS_DOM category
Added STRUCT_NCS_DOM_GEN category
Added equations to definitions of _phasing_MIR_der_shell.fom and
_phasing_MIR_shell.fom
Added REFINE_HIST category
========================================================================
Version 0.7.5 (1995-01-13)
------------------------------------------------------------------------
Changes (PMDF):
+ Provided for sequence microheterogeneity by making _entity_poly_seq.mon_id
part of the category key and by adding the data item
_entity_poly_seq.hetero as a flag
Added ENTITY_POLY_SEQ_DIF category - this meant adjusting some pointer
in referenced data items.
Added _entity_mon_atom.alt_atom_id.
Added COMP_PROG category
Removed non-c91 COMPUTING data items (phasing averaging, MAD, MIR and MR)
========================================================================
Version 0.7.6 (1995-01-17)
------------------------------------------------------------------------
Changes (PMDF):
+ Added ENTITY_SRC_NAT category
Added ENTITY_SRC_GEN category
Added ENTITY_NAM_COM category
Added ENTITY_NAM_SYS category
Added _entity.src_method data item
Moved other entity data items to new categories as appropriate
========================================================================
Version 0.7.7 (1995-01-18)
------------------------------------------------------------------------
Changes (PMDF):
+ Added PHASING_MIR_REFLN category
========================================================================
Version 0.7.8 (1995-01-25)
------------------------------------------------------------------------
Changes (PMDF):
+ Added _entity_mon.type, _entity_mon.number_atoms_all,
_entity_mon.number_atoms_nh, _entity_mon.one_letter_code
Added _entity_mon_angle.value_angle_esd, _entity_mon_angle.value_dist_esd,
_entity_mon_bond.value_dist_esd
Added _entity_mon_atom.type_energy, but since this is intended to be a
pointer to a category (_atom_type_energy) that doesn't exist yet, have
left it commented out
Added _entity_mon_chir.volume_three, _entity_mon_chir.volume_three_esd and
_entity_mon_chir.volume_flag
Added _entity_mon_plane.number_atoms_all, _entity_mon_plane.number_atoms_nh
Added _entity_mon_chir.number_atoms_all, _entity_mon_chir.number_atoms_nh
Added _entity_mon_chir_atom.dev
Added _entity_mon_tor_value.angle_esd, _entity_mon_tor_value.dist_esd
Added ENTITY_LINK category
Added ENTITY_LINK_ANGLE category
Added ENTITY_LINK_BOND category
Changes (HB et al.):
+ Added STRUCT_MON_NUCL category
Changes (PMDF):
+ Added label links from STRUCT_MON_NUCL to rest of dictionary
Added label links from STRUCT_MON_PROT as well (forget them initially)
========================================================================
Version 0.7.9 (1995-01-30)
------------------------------------------------------------------------
Changes (PMDF):
+ Fixed syntax errors unearthed by checking of JW and PDB
========================================================================
Version 0.7.10 (1995-02-03)
------------------------------------------------------------------------
Changes (PMDF):
+ Removed loop_ construction from loop_ or order one, except not for
category examples and not for parent/child loops
Standardized style of yes/no enumeration lists
Made style of all enumeration lists more standard (still not happy here)
Standardized style of examples
Standardized style of references in definitions
Began standardizing style of equations in definitions
========================================================================
Version 0.7.11 (1995-02-07)
------------------------------------------------------------------------
Changes (PMDF):
+ Finished standardizing style of equations in definitions
Moved ITEM_TYPE_LIST to bottom of dictionary
Moved ITEM_UNITS_LIST to bottom of dictionary
Moved ITEM_STRUCTURE_LIST to bottom of dictionary
Moved DICTIONARY_HISTORY to bottom of dictionary (it will come back up
to the top with version 1.0.0)
Rewrote dictionary header comments to reflect this dictionary
========================================================================
Version 0.7.12 (1995-02-09)
------------------------------------------------------------------------
Changes (JDW):
+ Changed _atom_site.label_res_id to _atom_site.label_comp_id which is
a child of _chem_comp.id.
+ Changed all children items named label_res_id to label_comp_id
+ Changed descriptions of many label_comp_id to reference correct
parent item. (_atom_site.label_comp_id rather than comp_comp.id).
+ Changed ENTITY_MON to CHEM_COMP and removed polymer component specific
terminology.
+ Changed ENTITY_LINK to CHEM_LINK and removed polymer component specific
terminology.
+ Added data type for yyyy-mm-dd and applied this where appropriate.
+ Added chem_comp_group and chem_link_group to the category group list.
+ Added '_' prefix to all data item save frame names.
========================================================================
Version 0.7.13 (1995-04-20)
------------------------------------------------------------------------
Changes (PMDF):
+ Changed all matrices back to element by element representation.
+ Reworded definitions of B and U matrices to clarify alternate exclusive
relationship
+ Changed 'miller' to 'Miller' in some definitions, but left it 'miller' in
data values.
+ Changed 'CIF' to 'data bock' where appropriate.
+ Made changes according to notes from last Rutgers meeting. Mostly this is
clearer wording of definitions.
Made formal Ref: for scattering factors.
Changed atom_site.description to atom_site.details
Expanded definitions for the components of the atom site label.
Added disclaimer to some records in ATOM_SITE and ATOM_SITES categories.
Changed _atom_type.analytical_mass_% to
_atom_type.analytical_mass_percent
Expanded definition of AUDIT category
Added separate esd data items to examples in CELL category
Added real formula in definition of _cell.volume
Moved disclaimer to the top in CHEMICAL categories
Changed enumeration to example in _chem_comp.one_letter_code
Changed _phasing_MIR_refln.F_sigma to _phasing_MIR_refln.F_meas_sigma
and adjusted definition to style of other esd definitions. Added type
condition esd to _phasing_MIR_refln.F_meas
Changed refln.observed_status to refln.status in example
Changed _refln.F_sigma to _refln.F_meas_sigma and adjusted definition to
style of other esd definitions. Added type condition esd to
_refln.F_meas
========================================================================
Version 0.7.14 (1995-05-03)
------------------------------------------------------------------------
Changes (PMDF):
+ Fixed definitions of _phasing_MIR_refln.index_k and
_phasing_MIR_refln.index_l
========================================================================
Version 0.7.15 (1995-05-18)
------------------------------------------------------------------------
Changes (PMDF):
+ Added DDL linking data names that are value to the data names that are
esds of those values
Changed _geom_bond.distance to _geom_bond.dist and _geom_bond.distance_esd
to _geom_bond.dist_esd
Changed _geom_contact.distance to _geom_contact.dist and
_geom_contact.distance_esd to _geom_contact.dist_esd
Changed _cell_measurement.temperature to _cell_measurement.temp and
_cell_measurement.temperature_esd to _cell_measurement.temp_esd
Changed _diffrn.ambient_temperature to _diffrn.ambient_temp and
_diffrn.ambient_temperature_esd to _diffrn.ambient_temp_esd
========================================================================
Version 0.7.16 (1995-05-18)
------------------------------------------------------------------------
Changes (PMDF):
+ Added _item.name DDL to those data items that didn't have it
Wrote program to check that the added names were all correct
Fixed problems that turned up (including one missing . in
_diffrn_radiation_detector_details
========================================================================
Version 0.7.17 (1995-05-22)
------------------------------------------------------------------------
Changes (PMDF):
+ Added _phasing_MIR_refln.F_meas_au and _phasing_MIR_refln.F_meas_au_sigma
and adjusted appropriate _item.related DDL
Added _refln.F_meas_au and _refln.F_meas_au_sigma and adjusted as above
Added _phasing_MIR_refln.F_calc_au and adjusted as above
Added _refln.F_calc_au and adjusted as above
Added _refln.A_calc_au and adjusted as above
Added _refln.B_calc_au and adjusted as above
Added _refln.A_meas_au and adjusted as above
Added _refln.B_meas_au and adjusted as above
Changed _item_related.function_code from 'replace' to
'alternate_exclusive' in database_2 data items
Added _item_related DDL to appropriate _database data items
========================================================================
Version 0.7.18 (1995-07-20)
------------------------------------------------------------------------
Changes (JDW):
+ Added '_struct_biol_gen.symmetry' to the key on struct_biol_gen.
+ Changed category block to entry.
+ Added _dictionary.datablock_id
+ Replace publ_group and journal_group with category group named iucr_group
+ Added category group named pdb_group
+ Removed all the _atom_site.label references and repointed any
references to this item to _atom_site.id.
+ Added optional atom identifiers to all of the GEOM categories.
+ Added translation vector to transformations in ATOM_SITES
+ Created subcategories for matrices and vectors
+ Moved _struct.keywords to a new category STRUCT_KEYWORDS
+ Added pointer to exptl_crystal.id as part of key in
category EXPTL_CRYSTAL_GROW_COMP.
+ Restructured DATABASE_PDB_REMARK category
+ Changed alternate_exclusive to replaces and replacedby in
DATABASE and DATABASE_2
+ Restructured examples in _chem_comp.one_letter_code ...
+ Added data item _chem_comp.three_letter_code
+ Made atom_site.label_alt_id and its children an optional item
+ Changed item names _atom_sites.frac_tran_* _atom_site.frac_transf_*
and _atom_sites.Cartn_tran_* _atom_site.Cartn_transf_*
+ Changed the key of ATOM_SITE_ANISOTROP to _atom_site_anisotrop.id
+ Added all of the GEOM category atom label items to their appropriate
parent data items.
+ 'arbitrary' added to list of item_units_list.code's
+ Fixed conflicting mandatory codes...
========================================================================
Version 0.7.19 (1995-07-23)
------------------------------------------------------------------------
Changes (JDW & PMDF):
+ Minor corrections in sheet example and version update.
+ Removed illegal characters from data item names.
Changed any "/" in data item names to "_over_".
========================================================================
Version 0.7.20 (1995-08-02)
------------------------------------------------------------------------
Changes (PMDF):
+ Enforced 80 character per line limit throughout.
+ Realphabetized _geom_angle.value and _geom_angle.value_esd.
+ Realphabetized _geom_torsion.value and _geom_torsion.value_esd.
+ Removed trailing blanks.
+ Fixed a couple of problems with missing terminal '.
========================================================================
Version 0.7.21 (1995-08-08)
------------------------------------------------------------------------
Changes (PMDF):
+ Added _citation_author.ordinal and updated examples to reflect this
addition.
+ Changed _item.mandatory_code for _citation_author.name to 'yes'.
+ First pass at checking the dictionary for spelling - lots of little
changes in lots of places.
+ Removed many occurrences of 'with with' in definitions.
========================================================================
Version 0.7.22 (1995-08-09)
------------------------------------------------------------------------
Changes (PMDF):
+ Added definitions for _chem_link_angle.link_id and
_chem_link_bond.link_id
+ Straighted out spacing inconsistencies with _item.mandatory_code
+ Another quick pass at spell checking
========================================================================
Version 0.7.23 (1995-08-10)
------------------------------------------------------------------------
Changes (PMDF):
+ Changed _struct_sheet_gen.label_seq_id to _struct_site_gen.label_seq_id
in _atom_site.label_seq_id tree
+ Removed duplicate entry of _phasing_MIR.entry_id in _entry.id tree
+ Removed alias in definitionof _refln.A_meas_au
+ Removed _item.category_id from
_chem_link.type_comp_1
_chem_link.type_comp_2
_phasing_mad_clust.expt_id
_phasing_mad_set.clust_id
_phasing_mad_set.expt_id
_phasing_mad_set.set_id
_phasing_mad_ratio.expt_id
_phasing_mad_ratio.clust_id
_phasing_mad_ratio.wavelength_1
_phasing_mad_ratio.wavelength_2
+ Removed _item_type.code from most of the above (it wasn't there in all
of them).
+ Added _item.mandatory_code to _phasing_mir_der.der_set_id
+ Corrected _item.name for _phasing_mad_ratio.wavelength_2
========================================================================
Version 0.7.24 (1995-08-21)
------------------------------------------------------------------------
Changes (PMDF):
+ Corrected category.id for data items in the DIFFRN_STANDARDS category
+ Corrected category.id for data items in the PHASING_MAD_EXPT category
+ Corrected category.id for selected data items in the PHASING_SET
category
+ Corrected alias for _atom_site.thermal_displace_type
+ Introduced alias of _atom_site_aniso_label for _atom_site_anistrop.id
+ Introduced alias of _atom_site_aniso_type_symbol for
_atom_site_anisotrop.type_symbol
========================================================================
Version 0.7.25 (1995-08-31)
------------------------------------------------------------------------
Changes (PMDF):
+ Eliminated duplicate line in _entry_id parent/child table
+ Changed the three occurrences of _item_type.code text to char
_atom_sites_alt.details
_atom_sites_alt_ens.details
_database_PDB_remark.text
+ Fixed Klyne and Prelog reference in GEOM_TORSION category description
+ Added data item _chem_comp_chir.atom_config
+ Added hyphen in non-crystallographic in definition sof
_struct_ncs_ens.point_group
+ Changed Data Base to Database when referring to the CSD
+ Fixed four occurrances of 'the the' in definitions
+ Added _item_range.maximum and _item_range.minimum DDL items to
_refine.ls_abs_structure_Flack and removed discussion of limits from
the definition.
+ Changed two occurances of 'will be' to 'are' in the definition of
_entity.type.
+ Changed ENTITY_NPOL to CHEM_COMP in definition of _entity.type.
+ Changes ATOM to HETATM for APS coordinates in Example 1 for the
ATOM_SITE category
+ Corrected _item.category_id for _struct_mon_details.prot_cis.
+ Corrected _item.category_id for _refine_hist.details.
+ Rewrote header comments to emphasize use of the mmCIF listserver as the
forum for the dictionary review process.
========================================================================
Version 0.7.26 (1995-09-25)
------------------------------------------------------------------------
Changes (PMDF):
+ Put single quotes around 5HVP in those examples where they were missing.
+ Fixed registration of '5VHP' in examples.
+ Fixed typos in definition of _diffrn_measurement.device_specific.
+ Added _item.name loop and parent-child tree to _chem_comp.type
+ Fixed _item.name for _phasing_mir_der.der_set_id
+ Fixed _item.name for _phasing_mir_der.native_set_id
+ Added _phasing_mir_der_refln.set_id to _item.name loops and parent-child
tree of _phasing_set.id
+ Fixed two misspellings of reference (refence).
========================================================================
Version 0.7.27 (1995-09-27)
------------------------------------------------------------------------
Changes (JDW & SH):
+ Added _item_aliases.dictionary and _item_aliases.version to all
alias items.
+ Added several missing aliases from cifdic.C94.
+ Added a few missing data type codes in chem_link_*
+ Modified all _item_range items to reflect the correction in
DDL 2.1.1. Checked all of the boundary conditions on ranges.
+ Made corrections in virtually all of the regular expressions.
+ Added data types 'ucode' and 'uchar'. These are case insensitive
character types for words and single line strings, respectively.
The regular expressions for these items will match characters
of upper and lower case but the primitive type is uchar so
all comparisons are performed in upper case. This avoids
problems with case, where case is really not important.
+ Reviewed all items with character data types and made the following
changes (hopefully uniformly):
- Data items with single word enumerates were set to type 'ucode'.
- Data items with multi word enumerates were set to type 'uchar'.
- Any item which could potentially exceed 80 characters was
set to type text.
- Items which are restricted to single words were set to type 'code'.
- Items which are short strings which may not span lines were
set to type 'char'.
+ Moved aliases for anisotropic temperature factors from category
ATOM_SITE to ATOM_SITE_ANISOTROP
+ Added category DATABASE_PDB_MATRIX to hold the SCALE and ORIGX
matrices/vectors.
+ Modified the defintions of data types 'char1' and 'char3' to
permit leading '+' to indicate a modification.
+ Checked dictionary with SIFLIB and returned to Paula ...
========================================================================
Version 0.7.28 (1995-10-06)
------------------------------------------------------------------------
Changes (PMDF):
+ Removed loop from category example for DATABASE_2
+ Fixed data names in category example for STRUCT_KEYWORDS
+ Rewrote enumeration list for _struct_conf_type.id
+ Removed references to chemical_formula.appendix and replaced them with
reference to the CHEMICAL_FORMULA category description
+ Added data items _chem_comp.formula and _chem_comp.formula_weight
+ Changed _chem_link_angle.atom_1_atom_id to _chem_link_angle.atom_id_1
+ Changed _chem_link_angle.atom_2_atom_id to _chem_link_angle.atom_id_2
+ Changed _chem_link_angle.atom_3_atom_id to _chem_link_angle.atom_id_3
+ Changed _chem_link_bond.atom_1_atom_id to _chem_link_bond.atom_id_1
+ Changed _chem_link_bond.atom_2_atom_id to _chem_link_bond.atom_id_2
+ Realphabetized to accomodation the above changes
+ Added CHEM_LINK_CHIR category
+ Added CHEM_LINK_CHIR_ATOM category
+ Added CHEM_LINK_PLANE category
+ Added CHEM_LINK_PLANE_ATOM category
+ Added CHEM_LINK_TOR category
+ Added CHEM_LINK_TOR_VALUE category
+ Added entries to parent/child table for _chem_link.id for reflect the
addition of the new categories.
+ Added Engh and Huber/Priestle examples to CHEM_LINK_BOND and
CHEM_LINK_ANGLE
+ Realphabetized categories in PHASING_MAD section
Changes (JDW):
+ Added _item_type.code's for _chem_link_chir*.atom_id and
_chem_link_tor.atom_id_*.
========================================================================
Version 0.7.29 (1995-12-11)
------------------------------------------------------------------------
Changes (PMDF):
+ Changes to my title and Brian's in header information.
+ Enhanced description of the 'Hill system' of element ordering in
the definition of _chem_comp.formula.
+ Added _item.mandatory_code to _phasing_mir_der.native_set_id
+ Added DATABASE_PDB_CAVEAT category.
+ Changed supercedes to superseded in DATABASE category description.
+ Changed DATABASE_NEW to DATABASE_2 in category description.
+ Changed SRUCT_SHEET_TOPOLOGY to STRUCT_SHEET_TOPOLOGY in category
description.
+ Changed examples for STRUCT_SHEET_RANGE to contain only
_struct_sheet_range.symmetry, not _struct_sheet_range.beg_symmetry and
_struct_sheet_range.end_symmetry
+ Added cell.Z_PDB data item
+ Changed _atoms_sites.Cartn_tran_matrix to atom_sites.Cartn_transf_matrix
in definition of _atom_sites.Cartn_transform_axes
+ Changed _chem_comp.nstd_class to _chem_comp.mon_nstd_class in
definition of _chem_comp.mon_nstd_flag
+ Added data items for _chem_link_bond.value_angle and
_chem_link_bond.value_angle_esd
+ Changed reference to _chemical_formula.appendix to CHEMICAL_FORMULA
category description in definition of _chemical_formula.moiety
+ Changed _comp.prog.version to _comp_prog.version and
_comp.prog.citation_id to _comp_prog.citation_id in COMP_PROG example
+ Changed reference to _computing.phasing_mir in _phasing_mir.method to
a reference to the COMP_PROG category.
Similarly with _computing.phasing_averaging in
_phasing_averaging.method and _computing.phasing_mad in
_phasing_mad.method and _computing.save_reduction in
_reflns.data_reduction_method
+ Changed _entity.name_com.name to _entity_name_com.name in
ENTITY_NAME_COM example
+ Changed reference to _exptl_crystal.face_ to data items in the
EXPTL_CRYSTAL_FACE category in the definition of
_exptl_crystal.description.
+ Changed _diffrn.attenuator_code to _diffrn_attenuator.code in
the definition of _diffrn_refln.attenuator_code
+ Changed _exptl.crystal_preparation to _exptl_crystal.preparation in the
definition of _exptl.details
+ Changed _geom_bond.distance to _geom_bond.dist in the definition of
_geom_bond.dist_esd
+ Added data items for _refine.ls_d_res_high and _refine.ls_d_res_low
+ Changed _refine.d_res_high to _refine.ls_d_res_high and
_refine.d_res_low to _refine.ls_d_res_low in the definition of
_refln.status
+ Changed _reflns_scale_group.code to _reflns_scale.group_code in the
definition of _refln.scale_group_code
+ Changed _struct_site_view_details to _struct_biol_view.details in the
rotation matrix element definitions in the STRUCT_BIOL_VIEW
category (even though I realize that this isn't really correct in
terms of the definition of _struct_biol_view.details)
+ Changed _symmetry.equiv_pos_as_xyz to _symmetry_equiv.pos_as_xyz in
the definition of _symmetry.space_group_name_H-M
+ Changed _struct_mon.details_RSSR to _struct_mon_details.RSSR and
_struct_mon.details_RSR to _struct_mon_details.RSR in a number of
definitions in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories
+ Changed _reflns_shell.possible_%_obs to _reflns_shell.percent_possible_obs
in the REFLNS_SHELL example
+ Corrected alphabetical order of data items in the REFLNS_SHELL category
+ Changed _struct_sheet.number_details to _struct_sheet.details in the
STRUCT_SHEET examples
+ Replaced _struct_sheet_range.beg_symmetry and
_struct_sheet_range.end_symmetry with _struct_sheet_range.symmetry
in the STRUCT_SHEET_RANGE category and fixed example itself
+ Changed _refine.ls_number_reflns to _refine.ls_number_reflns_obs in the
definitions of _refine.ls_restrained_S_all and
_refine.ls_restrained_S_obs
+ Changed _refine_ls_shell.reflns to _refine_ls_shell.number_reflns_obs in
the REFINE_LS_SHELL example
+ Removed example from DATABASE category as it was not longer valid
========================================================================
Version 0.7.30 (1996-01-29)
------------------------------------------------------------------------
Changes (PMDF, HB, JDW):
+ Added data items for pseudorotation in STRUCT_MON_NUCL.
+ Globally changed future tense usage to present tense (eg. will be -> is)
+ Added _citation.book_publisher_city.
+ Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD.
+ Added _citation.journal_coden_CAS.
+ Generalized the defintion of _atom_site.calc_flag.
+ Corrections to definitions defining beginning and ends of ranges in
category STRUCT_SHEET_HBOND.
+ Added data items _diffrn_refln.scan_rate and
_diffrn_refln.scan_time_backgd
+ Added HELX_LH_27_P and HELX_RH_27_P helix enumeration types.
+ Added figure of merit data item _refln.fom.
========================================================================
Version 0.7.31 (1996-02-12)
------------------------------------------------------------------------
Changes (JDW):
+ Added data items for _database_pdb_matrix.tvect_matrix[][] and
_database_pdb_matrix.tvect_vector[].
+ Generalized category CHEM_LINK to handle descriptions of a
any type of linkage. Created CHEM_COMP_LINK to describe
linkages between components, and ENTITY_LINK to describe
linkages between entities (and within entities between
nonsequential components). Both CHEM_COMP_LINK and ENTITY_LINK
reference the linkage description in the CHEM_LINK_* categories.
========================================================================
Version 0.7.32 (1996-02-17)
------------------------------------------------------------------------
Changes (JDW):
+ atom_site.entity_id renamed atom_site.label_entity_id.
+ atom_site.entity_seq_num deleted.
+ added items _atom_site.auth_asym_id, _atom_site.auth_atom_id,
_atom_site.auth_comp_id, and _atom_site.auth_seq_id. These
items provide placeholders for alternative nomenclature that
may be used by the author.
+ Set the parentage for _atom_site.label_seq_id to
_entity_poly_seq.num. All components of the atom site label
(_atom_site.label_*) are now linked to the mmCIF hierarchical
description of structure. The data items in _atom_site.auth_*
may be used by authors to provide alternative identifiers
in the atom site which conform with the scheme that is used in
the publication of the structure.
+ added category group mm_atom_site_auth_label
+ added auth_asym_id, auth_atom_id, auth_comp_id, and auth_seq_id
child data items to the categories: GEOM_ANGLE,GEOM_BOND,
GEOM_CONTACT, STRUCT_CONF, STRUCT_CONN, STRUCT_MON_NUCL,
STRUCT_PROT, STRUCT_PROT_CIS, STRUCT_NCS_DOM_GEN,
STRUCT_SHEET_HBOND, STRUCT_SHEET_RANGE, and STRUCT_SITE_GEN.
========================================================================
Version 0.7.33 (1996-02-19)
------------------------------------------------------------------------
Changes (JDW):
+ Replaced category COMP_PROG with category SOFTWARE supplied by
P. Bourne.
+ Fine tuned some values of _item_type.code. Fixed regular expression
for code and ucode.
========================================================================
Version 0.7.34 (1996-02-20)
------------------------------------------------------------------------
Changes (JDW):
+ Integrated STRUCT_REF, STRUCT_REF_SEQ and STRUCT_REF_SEQ_DIF from
PMDF.
+ Removed ENTITY_REFERENCE and ENTITY_POLY_SEQ_DIF.
+ Integrated modified categories STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM,
STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, and STRUCT_NCS_OPER from PMDF.
+ changed _item_type.code's 'char' and 'uchar' to 'line' and 'uline'.
========================================================================
Version 0.8.0 (1996-03-06)
------------------------------------------------------------------------
Changes (PMDF, HB, JDW):
+ Added unit type 8pi2_angstroms_squared B anisotropic temperature factors,
and added conversion factor for this new unit type in the
ITEM_UNITS_CONVERSION category.
+ Changed _item_type.code for _symmetry_equiv.id to 'code'
+ Added default value 'no' to _chem_comp.mon_nstd_flag.
========================================================================
Version 0.8.01 (1996-03-12)
------------------------------------------------------------------------
Changes (PMDF):
+ Added missing circumflex to definition of
_exptl_crystal.density_percent_sol.
+ Fixed erroneous reference to _atom_site.entity_seq_num in definition
of _atom_site.auth_seq_id.
+ Changed _chem_comp_link.id to _chem_link.id in definition of
_chem_comp_link.link_id.
+ Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD in
citation category example
+ Changed _entity_link.id to _chem_link.id in definition of
_entity_link.link_id.
+ Changed _chem_link.type_comp_1 to _chem_comp_link.type_comp_1 in
_item_name and parent/child tables for _chem_comp.type. The same change
was made for component 2.
========================================================================
Version 0.8.02 (1996-03-18)
------------------------------------------------------------------------
Changes (PMDF):
+ Changed category from chem_comp to chem_comp_link for data items
_chem_comp_link.type_comp_1 and _chem_comp_link.type_comp_1 in the
parent/child tree for the chem_comp.type data item.
+ Added _struct_ref_seq.seq_align_beg and _struct_ref_seq.seq_aling_end
to the mandatory code table for _entity_poly_seq.num.
+ Added _struct_ref_seq_dif.seq_num to both the parent/child and mandatory
code tables for _entity_poly_seq.num.
+ Added data item _struct_ncs_oper.code.
+ Changed units type to 8pi2_angstroms_squares for
_atom_site.B_iso_or_equiv and _atom_site.B_iso_or_equiv_esd.
+ Moved TVECT vector from DATABASE_PDB_MATRIX to
a new category DATABASE_PDB_TVECT and added a identifier
and details item to this new category. The matrix component of
TVECT has been removed.
========================================================================
Version 0.8.03 (1996-04-03)
------------------------------------------------------------------------
Changes (PMDF):
+ Began implementing changes to bring this dictionary into alignment
with the current version of the CIF core dictionary. These differences
were provided by Brian McMahon and I. David Brown. As most of these
changes are matters of style and not substance, they will not be noted
individually here. Anything that does involve substance will be.
+ Changed specification of the format of names to included that provision
for a dynanastic modifier.
========================================================================
Version 0.8.04 (1996-11-04)
------------------------------------------------------------------------
Changes (PMDF):
+ Changed format of references in data item definitions to match style of
extended core.
+ Changed format of matrices in data item definitions to match style of
extended core, with the addition of more rigorous definition of style
agreed to by PMDF, JDW and HB.
+ Changed format of equivations in data item definitions to match style of
extended core, with the addition of more rigorous definition of style
agreed to by PMDF, JDW and HB.
+ Added aliases to data items where they were missing to establish
correspondence with extended core.
+ Changed frac to fract in _atom_site.frac... data items.
+ Added _citation_editor_ordinal.
+ Added JOURNAL_INDEX data items, as well as _journal.language and
_journal.paper_category.
+ Added _diffrn_measurement_specimen_support
_diffrn_orient_refln_angle_omega
_diffrn_orient_refln_angle_theta
+ Added PUBL_BODY category and data items.
+ Added _publ.contact_author_address
_publ.contact_author_name
+ Added _publ.section_exptl_solution
_publ.section_synopsis
_publ.section_title_footnote
+ Added AUDIT_CONFORM category and data items.
+ Added GEOM_HBOND category and data items.
========================================================================
Version 0.8.05 (1996-11-11)
------------------------------------------------------------------------
Changes (PMDF):
+ More changes to bring this dictionary into alignement with the extended
core
+ Added _chemical_forumula.iupac
+ Added _atom_site.B_equiv_geom_mean (and its esd)
+ Added _atom_site.U_equiv_geom_mean (and its esd)
+ Added _atom_type.scat_length_neutron
========================================================================
Version 0.8.06 (1996-11-13)
------------------------------------------------------------------------
Changes (JDW):
+ Reorganized categories in the DIFFRN group to formally support
multiple diffraction data sets.
========================================================================
Version 0.8.07 (1996-12-18)
------------------------------------------------------------------------
Changes (PMDF):
+ Removed single quote from value of DDL items where they were not needed
+ Cleaned up style of range minimum/maximum data value
+ Cleaned up alignment of various DDL items
+ Deleted _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd
========================================================================
Version 0.8.08 (1997-01-06)
------------------------------------------------------------------------
Changes (PMDF):
+ Added R_work data items to the various REFINE categories
+ Rewrote definitions for existing R-factor definitions to distinguish
between R_work, R_free and conventional R
Changes (JDW) (retrieved from earlier, misplaced version):
+ Added data item _chem_comp.mon_nstd_parent_comp_id to provide explicit
reference between a nonstandard component and the parent component.
+ Changed _item_type.code for _chem_comp.id and all of its children
to 'ucode'.
+ Changed char3 and char1 to uchar3 and uchar1 to be consistent with
other case insensitive data type codes. Corrected the regular
expressions and primitive codes for these data types.
+ Added _chem_comp_atom.partial_charge.
+ Corrected the descriptions for _chem_comp_tor.comp_id,
_chem_comp_bond.comp_id and _chem_comp_angle.comp_id.
+ Added _chem_comp_tor_value.comp_id as a key for category
CHEM_COMP_TOR_VALUE.
+ Added _chem_comp_plane_atom.comp_id as a key in category
CHEM_COMP_PLANE_ATOM.
+ Miscellaneous corrections in item descriptions in CHEM_COMP_GROUP
categories.
+ Added item _chem_comp_plane_atom.dist_esd
========================================================================
Version 0.8.09 (1997-01-07)
------------------------------------------------------------------------
Changes (PMDF):
+ More changes to align with new core:
Changed _citation.book_coden_ISBN to _citation.book_id_ISBN
Changed _citation.journal_coden_ASTM to _citation.journal_id_ASTM
Changed _citation.journal_coden_CAS to _citation.abstract_id_ASTM
Changed _citation.journal_coden_CSD to _citation.journal_id_CSD
Changed _citation.journal_coden_ISSN to _citation.journal_id_ISSN
Changed _citation.medline_AN to _citation.database_id_Medline
Added _publ.requested_category
Corrected alias for _atom_type.scat_length_neutron
Added _journal.data_validation_number
Changed _diffrn_detector.detector_specific to _diffrn_detector.type
Deleted _diffrn_detector.detector_type
Added _diffrn_radiation.probe
Adjusted definition of _diffrn_radiation.type
Changed _diffrn_source.source_specific to _diffrn_source.type
Deleted old _diffrn_source.type
Changed _diffrn_radiation_wavelength.wavelength_wt to
_diffrn_radiation_wavelength.wt
Added _diffrn_radiation.xray_symbol
Aliased both versions 1.0 and 2.0 of the core for
_diffrn_detector.detector
_diffrn_detector.dtime
_diffrn_source.source
========================================================================
Version 0.8.10 (1997-01-22)
------------------------------------------------------------------------
Changes (PMDF):
+ Still more changes to align with new core:
Added _refine.ls_R_Fsqd_factor_obs
Added _refine.ls_R_I_factor_obs
Added _atom_site.disorder_assembly
Added new definition of _atom_site.disorder_group
Many more style and wording changes
Changes to provide compatibility with PDB Remark 3
Added _chem_comp_chir_atom.comp_id
Added _diffrn.ambient_temp_details
Added _exptl_crystal_grow.temp_details
Enlarged enumeration list of _phasing.method
Added _reflns.Rmerge_F_all
Added _reflns.Rmerge_F_obs
Added _reflns.B_iso_Wilson_estimate
Added _reflns.percent_possible_obs
Added _refine_ls_restr.weight
Added _refine.aniso_B data items
Added _exptl_crystal.density_matthews
Added _refine.ls_percent_reflns_R_free
Added _refine_ls_shell.percent_reflns_R_free
Added _refine.Luzzati_coordinate_error_obs
Added _refine.Luzzati_d_res_low_obs
Added _refine.Luzzati_sigma_a_obs
Added _refine.Luzzati_sigma_a_obs_details
Added _refine.Luzzati_coordinate_error_free
Added _refine.Luzzati_d_res_low_free
Added _refine.Luzzati_sigma_a_free
Added _refine.Luzzati_sigma_a_free_details
Added _refine.number_disordered_residues
Added _refine.occupancy_sum_hydrogen
Added _refine.occupancy_sum_non_hydrogen
========================================================================
Version 0.8.11 (1997-01-22)
------------------------------------------------------------------------
Changes (PMDF):
Enforced style of only one space at the end of a sentence and after a ;
Enforced stye in the categories section
Enforced style of Need example 1
+ More changes to provide compatibility for PDB Remark 3
Added _refine.B_iso_mean
Added _refine.ls_percent_reflns_obs
Added _refine.ls_R_factor_R_free_error
Added _refine.ls_R_factor_R_free_error_details
Added _refine_ls_shell.percent_reflns_obs
Added _refine_ls_shell.R_factor_R_free_error
Added _refine_ls_shell.redundancy_reflns_all
Added _refine_ls_shell.redundancy_reflns_obs
Added _refine.ls_redundancy_reflns_all
Added _refine.ls_redundancy_reflns_obs
Added _reflns.observed_criterion_sigma_F
Added _reflns.observed_criterion_sigma_I
Added REFINE_LS_RESTR_NCS category
Added _refine.solvent_model_details
Added _refine.solvent_model_param_bsol
Added _refine.solvent_model_param_ksol
========================================================================
Version 0.8.12 (1997-01-28)
------------------------------------------------------------------------
Changes (JDW):
Replaced all tabs with spaces.
Fixed instances of lines > 80 characters.
Added 'GLX' to the enumeration list for _chem_comp.three_letter_code.
Added 'B' and 'Z' to the enumeration list for
_chem_comp.one_letter_code.
Corrected definition for _cell_measurement.wavelength.
Corrected definitions for _atom_type.scat_dispersion_imag and
_atom_type.scat_dispersion_real.
Corrected examples for categories: CITATION, DIFFRN_DETECTOR,
DIFFRN_MEASUREMENT, DIFFRN_SOURCE, GEOM_HBOND, REFINE_ANALYZE,
REFINE_LS_RESTR,
Corrected definition for _reflns_shell.Rmerge_F_obs.
Corrected definition for _reflns_scale.group_code.
Changed _refine_ls_restr_ncs.weight_iso_B to
_refine_ls_restr_ncs.weight_B_iso.
Corrected definitions in: _diffrn_refln.angle_[chi-theta].
Using experimental data kindly provided by Tom Emge,
Shri Jain, Rachel Kramer, Jinsong Liu, and Gary Parkinson
examples were added for the following categories:
DIFFRN_ORIENT_MATRIX, DIFFRN_ORIENT_REFLN, DIFFRN_REFLN,
DIFFRN_SCALE_GROUP, EXPTL, EXPTL_CRYSTAL, EXPTL_CRYSTAL_FACE,
STRUCT_REF_SEQ, STRUCT_REF_SEQ_DIF, STRUCT_NCS_OPER,
STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS,
STRUCT_NCS_ENS_GEN, REFINE_LS_RESTR_NCS, PHASING_MIR_DER_REFLN,
PHASING_SET, PHASING_SET_REFLN, STRUCT_MON_NUCL, STRUCT_MON_PROT,
REFINE_HIST, ATOM_SITE_ANISOTROP, CHEM_COMP_LINK, JOURNAL, PUBL,
CELL_MEASUREMENT_REFLN, CHEMICAL, CHEMICAL_CONN_ATOM,
CHEMICAL_CONN_BOND, STRUCT_BIOL_VIEW, STRUCT_SITE_VIEW,
STRUCT_MON_PROT_CIS.
Added _exptl_crystal_face.crystal_id.
Added items: _reflns.observed_criterion_I_min
_reflns.observed_criterion_I_max
_reflns.observed_criterion_F_max
_reflns.observed_criterion_F_min.
Changed dictionary tile and data block name to the conforming
name recommended by SRH/BMcM, cif_mm.dic.
Restore consistency to the 'arbitrary units' suffix:
Changed _phasing_set_refln.F_meas_au_sigma to
_phasing_set_refln.F_meas_sigma_au
Changed _phasing_mir_der_refln.F_meas_au_sigma to
_phasing_mir_der_refln.F_meas_sigma_au
Changed _phasing_set_refln.F_meas_au_sigma to
_phasing_set_refln.F_meas_sigma_au
Changed _refln.F_meas_au_sigma to
_refln.F_meas_sigma_au
Although data item names and category names are not case
sensitive, as a matter of style certain abbreviations are
consistently expressed in upper case (e.g. B, MIR, MAD, PDB).
Corrected definition for category DATABASE.
Added category ENTRY_LINK and corresponding aliases to
CIF core category audit_link.
Corrected alias name _refine_ls_R_I_factor.
Added core CIF alias _diffrn_refln_crystal_id to data item
_diffrn.crystal_id.
========================================================================
Version 0.9.0 (1997-01-30)
------------------------------------------------------------------------
Changes (PMDF):
+ Corrected _reflns_observed_criterion to _reflns.observed_criterion in
a number of places
+ Aligned enumeration lists in this dictionary with those in version 2.0 of
the core dictionary. This involved changes in:
_citation.coordinate_linkage
_diffrn_radiation.xray_symbol
_diffrn_refln.scan_mode
_diffrn_refln.scan_mode_backgd
_exptl.absorpt_correction_type
_publ_manuscript_incl.extra_defn
_refine.ls_hydrogen_treatment
_refine.ls_structure_factor_coef
+ A number of corrections to errors pointed out by H. Bernstein
Added category.id to _database_PDB_tvect.id
Fixed spelling of _publ.section_exptl_soltuion
Corrected _refine.ls_R_factor_work to
_refine.ls_R_factor_R_work in description
Corrected spelling of _refine_analyze.Luzaatti_d_res_low_obs in example
Corrected spelling of _refine_analyze.Luzzatti_coordinate_error_obs in
example
Corrected _geom_hbond.atom_site_label_id_D to
_geom_hbond.atom_site_id_D in example
Corrected _geom_hbond.atom_site_label_id_H to
_geom_hbond.atom_site_id_H in example
Corrected _geom_hbond.atom_site_label_id_A to
_geom_hbond.atom_site_id_A in example
Corrected _entry_link.description to _entry_link.details
Corrected _DIFFRN_SCALE_GROUP to DIFFRN_SCALE_GROUP in description
Corrected _refine_ls_restr_ncs.model_details to
_refine_ls_restr_ncs.ncs_model_details in example
Corrected _refln.observed_criterion to _reflns.observed_criterion in
description
Corrected _struct_biol_view.view_id to _struct_biol_view.id in example
Corrected _chem_comp_link.id to _chem_comp_link.link_id in example
Corrected _chem_comp_link.comp_type_1 to
_chem_comp_link.type_comp_1
Corrected _chem_comp_link.comp_type_1 to
_chem_comp_link.type_comp_1
Corrected _entry_link.link_id to _entry_link.entry_id in description
Changes (JDW):
Corrections to REFINE_HIST category example and removal of a
few misplaced colons.
========================================================================
Version 0.9.01 (1997-01-31)
------------------------------------------------------------------------
Changes (PMDF):
+ Removed occurrance of two or more blank lines
+ Enforced rule of no apostrophes around values for _item_sub_category.id
+ Enforced rule of no apostrophes around values for_item_default.value
+ Enforced rule of no apostrophes around values for_item.mandatory_code
and fixed one alignment problem
+ Enforced rule of no apostrophes around values for
_item_related.function_code and fixed a few alignment problems
+ Added _item.mandatory_code for _diffrn_refln.wavelength_id
+ Changed cifdic.c94 to cif_core.dic in _item_aliases.dictionary everywhere
+ Changed 2.0 to 2.0.1 in _item_aliases.version everywhere
+ Changed to consistent usage of kelvins instead of kelvin, got rid of
capitalized versions
+ Removed capitalized usages of angstroms
+ Enforced rule of no apostrophes around values for _item_units.code
+ Fixed alignment problems with a few _category_key.name values
========================================================================
Version 1.0.00 (1997-10-14)
------------------------------------------------------------------------
Changes (PMDF):
+ Editorial changes in light of proof-reading by B. McMahon and I.D. Brown
+ No data names or enumeration values have changed, with the exception
of the addition of the enumeration value 'other' to exptl.method
+ The bulk of the changes, which are too numerous to list there, were
fixing spelling and grammar errors, and providing missing definitions
+ In a few cases, data definitions were reworded for clarity
+ Replaced erroneous occurances of Y~calc~ with Y~obs~ in the defintions of
weighted R factors (Ian Tickle)
========================================================================
Version 2.0.01 (2000-10-17)
------------------------------------------------------------------------
Changes (JDW):
+ Integrated new definitions and extensions to existing categories.
Additional data definitions submitted by Kim Henrick. Content
of phasing definitions reviewed by Paula Fitgerald. Content
of refinement definitions reviewed by Dale Tronrud. Editorial
review by Helen Berman, John Westbrook, and Paula Fitzgerald.
New Items included in this version:
_phasing_MIR.d_res_high, _phasing_MIR.d_res_low, _phasing_MIR.FOM,
_phasing_MIR.FOM_acentric, _phasing_MIR.FOM_centric, _phasing_MIR.reflns,
_phasing_MIR.reflns_acentric, _phasing_MIR.reflns_centric,
_phasing_MIR.reflns_criterion, _phasing_MIR_der.power_acentric,
_phasing_MIR_der.power_centric, _phasing_MIR_der.R_cullis_acentric,
_phasing_MIR_der.R_cullis_anomalous, _phasing_MIR_der.R_cullis_centric,
_phasing_MIR_der.reflns_acentric, _phasing_MIR_der.reflns_anomalous,
_phasing_MIR_der.reflns_centric, _phasing_MIR_der_site.occupancy_anom,
_phasing_MIR_der_site.occupancy_anom_su, _phasing_MIR_der_site.occupancy_iso,
_phasing_MIR_der_site.occupancy_iso_su, _phasing_MIR_shell.FOM_acentric,
_phasing_MIR_shell.FOM_centric, _phasing_MIR_shell.reflns_acentric,
_phasing_MIR_shell.reflns_anomalous, _phasing_MIR_shell.reflns_centric,
_refine.correlation_coeff_Fo_to_Fc, _refine.correlation_coeff_Fo_to_Fc_free,
_refine.overall_SU_B, _refine.overall_SU_ML,
_refine.overall_SU_R_Cruickshank_DPI, _refine.overall_SU_R_free,
_refine.overall_FOM_free_R_set, _refine.overall_FOM_work_R_set,
_refine_analyze.RG_d_res_high, _refine_analyze.RG_d_res_low,
_refine_analyze.RG_free, _refine_analyze.RG_work, and
_refine_analyze.RG_free_work_ratio.
+ New categories included in this version:
REFINE_FUNCT_MINIMIZED,REFINE_LS_RESTR_TYPE, REFLN_SYS_ABS.
+ Modification of examples for _refine_ls_restr.type
+ Contributed editorial and typographical corrections.
+ Corrected incomplete keys in categories PHASING_MAD_SET and
DATABASE_PDB_REV_RECORD.
+ _exptl.method enumerations moved to examples.
+ Added database codes for RCSB and EBI.
+ Fixed item examples in _publ_body.label.
========================================================================
Version 2.0.02 (2000-10-24)
------------------------------------------------------------------------
Changes (JDW):
+ Updated enumerations for _database_PDB_rev.mod_type.
+ Updated enumerations for _struct_conn_type.id
+ Corrected data type of _refine_ls_shell.percent_reflns_obs
from int to float
+ Updated preliminary description of _database_PDB_rev.status.
+ Changed regular expression for float to accept trailing decimal (ie. dd.)
+ Add () to regular expressions for code and ucode.
+ Added L-saccharide, D-saccharide, saccharide to enumerants for
_chem_comp.type to handle monosaccarided components where linking
cannot be inferred.
========================================================================
Version 2.0.03 (2000-11-09)
------------------------------------------------------------------------
Changes (JDW):
+ Relax regular expression for atom names to accept blanks in atom names
in order to support nomenclature used in many existing macromolecular
data files. Data type "atcode" has been assigned to
_chem_comp_atom.atom_id, _atom_site.auth_atom_id and all related items.
========================================================================
Version 2.0.04 (2004-04-21)
------------------------------------------------------------------------
Changes (JDW):
+ Changed working name and packaging of dictionary.
+ _reflns_shell_number_possible range data type error fixed
+ Fix syntax errors in category examples.
+ Remove nonsense zero value default values
+ Remove all default values from *_esd items
+ Make _atom_site.label_* mandatory
+ Make _atom_site.auth_asym_id mandatory
+ Make _software.citation_id optional
========================================================================
Version 2.0.05 (2004-08-04)
------------------------------------------------------------------------
Changes (JDW):
+ Changed data type of _refine.ls_redundancy_reflns_all,
_refine.ls_redundancy_reflns_obs,
_refine_ls_shell.redundancy_reflns_all,
_refine_ls_shell.redundancy_reflns_obs
from int to float.
========================================================================
Version 2.0.06 (2005-03-03)
------------------------------------------------------------------------
Changes (JDW):
+ The following data items added to maintain data item correspondence
with the CIF CORE dictionary V 2.3. All aliases in section 1 updated
to version 2.3.
_atom_site.adp_type
_atom_site.refinement_flags
_atom_site.refinement_flags_adp
_atom_site.refinement_flags_occupancy
_atom_site.refinement_flags_posn
_atom_sites.special_details
_atom_type.scat_dispersion_source
_audit_link.block_code
_audit_link.block_description
_cell.reciprocal_angle_alpha
_cell.reciprocal_angle_beta
_cell.reciprocal_angle_gamma
_cell.reciprocal_angle_alpha_esd
_cell.reciprocal_angle_beta_esd
_cell.reciprocal_angle_gamma_esd
_cell.reciprocal_length_a
_cell.reciprocal_length_b
_cell.reciprocal_length_c
_cell.reciprocal_length_a_esd
_cell.reciprocal_length_b_esd
_cell.reciprocal_length_c_esd
_cell.special_details
_chemical.absolute_configuration
_chemical.melting_point_gt
_chemical.melting_point_lt
_chemical.optical_rotation
_chemical.properties_biological
_chemical.properties_physical
_chemical.temperature_decomposition
_chemical.temperature_decomposition_esd
_chemical.temperature_decomposition_gt
_chemical.temperature_decomposition_lt
_chemical.temperature_sublimation
_chemical.temperature_sublimation_esd
_chemical.temperature_sublimation_gt
_chemical.temperature_sublimation_lt
_citation.database_id_CSD
_database.CSD_history
_database.code_CAS
_database.code_CSD
_database.code_ICSD
_database.code_MDF
_database.code_NBS
_database.code_PDB
_database.code_PDF
_database.code_depnum_ccdc_fiz
_database.code_depnum_ccdc_journal
_database.code_depnum_ccdc_archive
_diffrn.ambient_pressure
_diffrn.ambient_pressure_esd
_diffrn.ambient_pressure_gt
_diffrn.ambient_pressure_lt
_diffrn.ambient_temperature
_diffrn.ambient_temperature_esd
_diffrn.ambient_temperature_gt
_diffrn.ambient_temperature_lt
_diffrn_attenuator.material
_diffrn_detector.area_resol_mean
_diffrn_detector.dtime
_diffrn_refln.class_code
_diffrn_refln.intensity_u
_diffrn_reflns.av_unetI/netI
_diffrn_reflns_class.av_R_eq
_diffrn_reflns_class.av_sgI/I
_diffrn_reflns_class.av_uI/I
_diffrn_reflns_class.code
_diffrn_reflns_class.description
_diffrn_reflns_class.d_res_high
_diffrn_reflns_class.d_res_low
_diffrn_reflns_class.number
_diffrn_source.take-off_angle
_diffrn_standards.scale_u
_exptl_crystal.colour_lustre
_exptl_crystal.colour_modifier
_exptl_crystal.colour_primary
_exptl_crystal.density_meas
_exptl_crystal.density_meas_esd
_exptl_crystal.density_meas_gt
_exptl_crystal.density_meas_lt
_exptl_crystal.density_meas_temp
_exptl_crystal.density_meas_temp_esd
_exptl_crystal.density_meas_temp_gt
_exptl_crystal.density_meas_temp_lt
_geom_bond.valence
_publ_author.id_iucr
_refine.ls_R_factor_gt
_refine.ls_goodness_of_fit_gt
_refine.ls_goodness_of_fit_ref
_refine.ls_shift/esd_max
_refine.ls_shift/esd_mean
_refine.ls_shift/su_max
_refine.ls_shift/su_max_lt
_refine.ls_shift/su_mean
_refine.ls_shift/su_mean_lt
_refine_ls_class.code
_refine_ls_class.d_res_high
_refine_ls_class.d_res_low
_refine_ls_class.R_factor_gt
_refine_ls_class.R_factor_all
_refine_ls_class.R_Fsqd_factor
_refine_ls_class.R_I_factor
_refine_ls_class.wR_factor_all
_refln.class_code
_refln.d_spacing
_refln.include_status
_refln.mean_path_length_tbar
_refln.observed_status
_refln.sint/lambda
_reflns.Friedel_coverage
_reflns.number_gt
_reflns_class.code
_reflns_class.description
_reflns_class.d_res_high
_reflns_class.d_res_low
_reflns_class.number_gt
_reflns_class.number_total
_reflns_class.R_factor_all
_reflns_class.R_factor_gt
_reflns_class.R_Fsqd_factor
_reflns_class.R_I_factor
_reflns_class.wR_factor_all
_reflns_shell.meanI_over_sigI_gt
_reflns_shell.meanI_over_uI_all
_reflns_shell.meanI_over_uI_gt
_reflns_shell.number_measured_gt
_reflns_shell.number_unique_gt
_reflns_shell.percent_possible_gt
_reflns_shell.Rmerge_F_gt
_reflns_shell.Rmerge_I_gt
_space_group.crystal_system
_space_group.id
_space_group.IT_number
_space_group.name_Hall
_space_group.name_H-M_alt
_space_group_symop.id
_space_group_symop.operation_xyz
_space_group_symop.sg_id
_valence_param.atom_1
_valence_param.atom_1_valence
_valence_param.atom_2
_valence_param.atom_2_valence
_valence_param.B
_valence_param.details
_valence_param.id
_valence_param.ref_id
_valence_param.Ro
_valence_ref.id
_valence_ref.reference
Changes (BM): 2005-03-03
Editorial changes to accompany International Tables Volume G publication
(B. McMahon):
+ Fixed broken example loop for _phasing_MAD_ratio.*
+ Expanded the definitions for _phasing_MIR_der_refln.HL_A_iso (and B, C
and D terms) and provided literature reference
+ Abbreviation .FOM (for figure-of-merit) consistently rendered lowercase
+ Expanded the definitions for _refine.solvent_model_param_bsol (and
*_ksol) and provided literature reference
+ Rearranged the order of entries in the REFINE_ANALYZE category to
preserve strict alphabetisation
+ Removed _refine_ls_restr_type.U_sigma_weights from example in
REFINE_LS_RESTR_TYPE category
+ Commented out the incorrect example for the CHEM_COMP_LINK category
+ For the example in the ENTITY_NAME_SYS category supplied the EC
number and the systematic name "water"; also trimmed the irrelevant
last line of the definition.
+ Changed the vague 'x,x-pyranoside' example of _entity_name_sys.name
to 'hydroquinone-beta-D-pyranoside' and matched this with 'arbutin'
for _entity_name_com.name
+ Removed the CAVEAT and REMARK terms (and PDB code trailers) from the
contents pf the _database_PDB_caveat.* and *_remark.* examples in
accordance with current PDB practice
+ Updated reference to Tickle et al. in _refine_analyze.RG_free_work_ratio
+ Fixed few minor typos
+ Cosmetic reflowing of textual examples to aid typesetting
+ Added Engh & Huber and Priestle references to example details
+ Changed upper enumeration limit of _atom_site_attached_hydrogens to 8
in line with current Core dictionary
+ Added URL of PDB format description to _database_PDB_rev.mod_type
+ Extended enumeration list of _publ.requested_category for Acta E papers
+ Updated definition of _refine.ls_abs_structure_Flack and *_Rogers to
reflect the more correct wording of the current Core dictionary.
+ Added _item_range.maximum and *minimum to _refine.ls_abs_structure_Rogers
in line with new wording of definition.
Changes (NJA): 2005-03-03
+ Commented out duplicate save frames for following items with
_item_aliases.version 2.0.1:
_atom_site.refinement flags, _database.code_CAS, _database.code_CSD
_database.code_ICSD, _database.code_MDF, _database.code_NBS
_database.code_PDF, _diffrn.ambient_pressure, _diffrn.ambient_pressure.esd
_diffrn_detector.dtime, _exptl_crystal.density.meas
_exptl_crystal.density_meas_temp, _refln.mean_path_length_tbar
Changes (BM): 2005-03-03
+ Fixed erroneous _item.name in save__diffrn.ambient_pressure_esd
+ Removed erroneous aliases to *_esd quantities in coreCIF 2.3:
_cell_reciprocal_angle_alpha_esd, _cell_reciprocal_angle_beta_esd
_cell_reciprocal_angle_gamma_esd, _cell_reciprocal_length_a_esd
_cell_reciprocal_length_b_esd, _cell_reciprocal_length_c_esd
_chemical_temperature_decomposition_esd
_chemical_temperature_sublimation_esd
_diffrn.ambient_pressure_esd, _diffrn_ambient_temperature_esd
_exptl_crystal_density_meas_esd, _exptl_crystal_density_meas_temp_esd
+ Removed redundant aliases:
_cell.special_details ( = _cell.details)
_diffrn.ambient_temperature ( = _diffrn.ambient_temp)
_refine.ls_shift/esd_max ( = _refine.ls_shift_over_esd_max)
_refine.ls_shift/esd_mean ( = _refine.ls_shift_over_esd_mean)
_refln.observed_status ( = _refln.status)
_refln.sint/lambda ( = _refln.sint_over_lambda)
+ Changed _refine.ls_shift/su_max to _refine.ls_shift_over_su_max
and likewise for *_lt, *_mean and *_max_lt
Changes (NJA): 2005-03-07
+ Changed _reflns.class_d_res_low to _reflns_class.d_res_low in description of
_reflns_class.wR_factor_all
+ Added [][] to _atom_sites.Cartn_transf_matrix, _diffrn_reflns.transf_matrix
and _diffrn_orient_matrix.UB for consistency throughout.
+ Changed _chem_comp_link.type_1 and _2 to _chem_comp_link.type_comp_1
and 2 in _chem_link_angle.atom_id_1 and _2
+ Changed all occurences of _diffrn.ambient_temperature to _diffrn.ambient_temp
+ Changed _diffrn_reflns.class_code to _diffrn_reflns_class.code in
_diffrn_refln.class_code
+ Changed _geom_bond.distance to _geom_bond.dist in description of
_geom_bond.valence.
+ Changed _refln.observed_status to _refln.status in refln.include_status
+ Changed _reflns.special_details to _reflns.details in _reflns.number_gt and
_reflns_class.number_gt
+ Created new entry for _reflns.threshold_expression, as no entry existed and
many item descriptions referred to _reflns_threshold_expression (these were
then changed to _reflns.threshold_expression).
+ Changed _struct_mon_prot.alt_id, _struct_mon_prot.asym_id,
_struct_mon_prot.comp_id and _struct_mon_prot.seq_id to
_struct_mon_prot.label_alt_id, _struct_mon_prot.label_asym_id,
_struct_mon_prot.label_comp_id and _struct_mon_prot.label_seq_id
in Example 1 of _struct_mon_prot.
+ Changed _struct_site_view.view_id to _struct_site_view.id in Example 1
of _struct_site_view.
========================================================================
Version 2.0.07 (2005-03-03)
------------------------------------------------------------------------
Changes (JDW) 2005-03-08
+ Changed related references to _diffrn.ambient_temperature to
_diffrn.ambient_temp
+ Changed related references to _refln.observed_status to
_refln.status
+ Restore original case to FOM - although case is not an issue for
mmCIF it is an issue for XML translations.
========================================================================
Version 2.0.08 (2005-04-06)
------------------------------------------------------------------------
Changes (JDW) 2005-04-06
+ Added mandatory code _cell.reciprocal_angle_beta
========================================================================
Version 2.0.09 (2005-06-27)
------------------------------------------------------------------------
Internal dates used for housekeeping prior to release
2005-04-13
Changes (NJA) 2005-04-13
+ Minor corrections to spelling and punctuation.
+ pdb_group definition: Brookhaven Protein Data Bank changed to
Protein Data Bank.
2005-04-14
Changes (NJA) 2005-04-14
+ Minor corrections to spelling and punctuation.
+ _atom_sites.solution_* descriptions edited so each appropriate
to the particular data name.
+_chem_comp.formula description edited to match that in core dictionary
+_chem_comp.three_letter_code: several typing errors in amino-acid and
base names corrected.
+_chem_comp_atom.model_Cartn_z: 'The x component ...' changed to
'The z component...'
+_chemical.melting_point_* descriptions edited so each appropriate to the
particular data name.
+_chemical.temperature_decomposition_* descriptions edited so each
appropriate to the particular data name.
+_chemical.temperature_sublimation_* descriptions edited so each appropriate
to the particular data name.
2005-04-15
Changes (NJA) 2005-04-15
+ Minor corrections to spelling and punctuation.
+_citation.journal_id_CSD description, Brookhaven Protein Data Bank
changed to Protein Data Bank.
+_database.code_* entries edited so each is relevant to the particular
data name
+_database_PDB_matrix.scale[3][3]: description changed from 'The [1][1]
element of the PDB SCALE matrix.' to 'The [3][3] element of the PDB SCALE
matrix.'
+_diffrn.ambient_pressure_gt and _lt, descriptions edited so each is
relevant to the particular data name.
+_diffrn.ambient_temp_gt and _lt, descriptions edited so each is relevant
to the particular data name.
+_diffrn_attenuator.scale description changed to match that in the core
dictionary.
+_diffrn_radiation_wavelength.id: _diffrn_radiation_wavelength in description
changed to _diffrn_radiation_wavelength.wavelength
+_diffrn_reflns_class.av_sgI/I description [sum|u(net I)|/sum|net I|] changed
to [sum|sigma(net I)|/sum|net I|]
+_diffrn_reflns_class.d_res_high and _low descriptions changed to match
those in the core dictionary
+diffrn_source Example 1 _diffrn_source.power '50 kw, 180 mA' changed to
_diffrn_source.power 50 and _diffrn_source.current 180
+_exptl_crystal.density_Matthews year of reference corrected from 1960 to
1968
+_exptl_crystal.density_meas_gt and _lt descriptions edited so each is
relevant to the particular data name.
+_exptl_crystal.density_meas_temp_gt and _lt descriptions edited so each
is relevant to the particular data name.
+geom_contact and geom_bond Example 1 year for reference corrected from
1991 to 1992
+_phasing_MAD_ratio.d_res_high and low ; _phasing_MAD_set.d_res_high
and _low; _phasing_MIR.d_res_high and low; _phasing_MIR_der.d_res_high
and low; _phasing_MIR_der_shell.d_res_high and low;
_phasing_MIR_shell.d_res_high and low and _refine.ls_d_res_high and low
rephrased to correspond to similar terms in the core dictionary.
+Spelling of Lattman corrected in references to Hendrickson, W. A. &
Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
+Temperature factor replaced by displacement parameter throughout.
+refine Example 2 _refine.ls_weighting_scheme
'calc w=1/(\s^2^(F)+0.0004F^2^)' split into _refine.ls_weighting_scheme and
_refine.ls_weighting_details
+_refine.ls_extinction_coef and _refine.ls_extinction_method reference to
Becker and Coppens corrected to 129-147, 148-153 (is two articles).
+_refine.ls_restrained_S_all and _obs: Y~calc~ = the observed coefficients
changed toY~calc~ = the calculated coefficients
2005-04-18
Changes (NJA) 2005-04-18
+ Minor corrections to spelling and punctuation.
+ temperature factor changed to displacement parameter throughout
+ _refine_ls_class.R_factor_all 'and for significantly intense reflections
(see _reflns.threshold_expression) ' removed from description.
+ _refine_ls_class.R_factor_gt 'for all reflections' removed from
description.
+ _refine_ls_class.d_res_high and _low, _refine_analyze.RG_d_res_high
and _low, _refine_ls_shell.d_res_high and _low,
_reflns.d_resolution_high and low, _reflns_class.d_res_high and _low,
_reflns_shell.d_res_high and _low definitions edited to match related
definitions in the core dictionary
+ _refln.intensity_calc _meas, _sigma edited to match corresponding entries
in the core dictionary
+ _reflns.Friedel_coverage in description _reflns_number_total changed to
_reflns.number_all.
+ _reflns_class.R_factor_all 'and for significantly intense reflections (see
_reflns.threshold_expression)' removed from description.
+ _reflns_class.R_factor_gt 'all reflections, and for' removed from description
+ _reflns_class.number_total in description: _reflns_special_details
changed to _reflns.details
2005-04-19
Changes (NJA) 2005-04-19
+ Minor corrections to spelling and punctuation.
+ _valence_param.ref_id description: _valence_ref_id changed
to _valence_ref.id
+ References to International Tables updated.
2005-04-22
Changes (NJA) 2005-04-22
+ _cell.reciprocal_angle_alpha, beta and gamma: descriptions edited
so each appropriate to the particular data name.
+ _cell.reciprocal_length_a, b and c: descriptions edited so each
appropriate to the particular data name.
+ _struct_mon_nucl.chi1 and _chi2; descriptions edited from
`... sugar-base torsion angle chi...' to '... sugar-base torsion angle chi1'
and '... sugar-base torsion angle chi2'
2005-05-03
Changes (NJA) 2005-05-03
+ several data items *_esd edited so that the description reads
'the standard uncertainly of *', not 'the standard uncertainty of *_esd'
+ several DDL1 datanames in descriptions changed to DDL2 datanames
2005-05-10
Changes (NJA) 2005-05-10
+ _citation.journal_id_CSD example changed from 070 to 0070
+ Mursudov and Dodson (1997) references corrected
+ References to Cruickshank DPI updated
+ References to Luzzati (1952) corrected
2005-06-23
Changes (NJA) 2005-06-23
_publ_author.email added. Corrections for IT G Chapter 4.5 included.
2005-06-25 (BM)
ITEM_UNITS_LIST: cosmetic changes to definitions of some units
ITEM_UNITS_CONVERSION: multipliers in electrons per <unit> cubed terms fixed
2005-06-27 (BM)
Some minor editorial changes to ensure consistency with latest pdbx
dictionary version and ITG text. Only significant change:
+ in _citation.id the listing for _software.citation_id has
_item.mandatory_code changed to "no" to match the value in
save__software.citation_id and to match pdbx
========================================================================
International Tables for Crystallography
Volume G: Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon
![[International Tables Vol. G]](https://www.iucr.org/__data/assets/image/0014/11156/g.gif) |
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| sample pages | ||
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| CIF dictionaries |
An essential guide and reference to CIF for programmers, data managers handling crystal-structure information and practising crystallographers.
