[Imgcif-l] Proposed new imgCIF/CBF dictionary
Herbert J. Bernstein
yaya at bernstein-plus-sons.com
Sun Jul 3 04:05:31 BST 2011
Dear Colleagues,
The most recently COMCIFS-approved imgCIF/CBF dictionary dictionary
is the 2005 1.3.2 version at ftp://ftp.iucr.org/pub/cif_img.dic
A great deal of work has been done since then. This would be a
good time to initiate the formal process of submitting a new
imgCIF/CBF dictionary to COMCIFS for approval.
You will find the most recent draft dictionary at:
http://www.bernstein-plus-sons.com/software/CBF/doc/cif_img_1.6.4.html
http://www.bernstein-plus-sons.com/software/CBF/doc/cif_img_1.6.4.dic
http://downloads.sf.net/cbflib/cif_img_1.6.4_2Jul11.dic
You will find the line-by-line differences between the last-approved
version and the current draft at
http://downloads.sf.net/cbflib/cif_img_1.3.2_1.6.4.diff
A summary of the major changes follows below my signature. Please
provide comments, corrections and suggestions to this list between now
and 15 August 2011.
Note that a 0.9.2.2 CBFlib kit including this draft dictionary
has been posted to sorrceforge at
http://downloads.sf.net/cbflib/CBFlib-0.9.2.2.tar.gz
Regards,
Herbert
1.6.4 2011-07-02
; Corrections to support DLS Dectris header as per G. Winter (HJB)
+ Define new tags _diffrn_scan.time_period,
_diffrn_scan.time_rstrt_incr,
_diffrn_scan_frame.time_period,
_diffrn_scan_frame.time_rstrt_incr
+ fix bad category name in loop in _diffrn_detector.id
+ remove stray text field terminator at line 4642
+ fix unquoted tag as a value in _diffrn_scan_frame_monitor.id
+ make formerly mandatory and implicit deprecated items non-mandatory
;
1.6.3 2010-08-26
; Cummulative corrections from 1.6.0, 1, 2 drafts (HJB)
+ Move descriptive dictionary comments into
_datablock.description with catgeory tree described
+ add default _array_data.array_id value of 1
+ add option of CBF_BACKGROUND_OFFSET_DELTA compression
+ add VARIANT catgeory and tags
+ add DIFFRN_SCAN_FRAME_MONITOR category
;
1.5.4 2007-07-28
; Typographics corrections (HJB)
+ Corrected embedded degree characters to \%
+ Corrected embedded Aring to \%A
+ Added trailing ^ for a power
+ Removed 2 cases of a space after an underscore
in tag name.
;
1.5.3 2007-07-08
; Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
;
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to definitions for the binary data type to handle new compression
types, maps, and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
--
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
yaya at dowling.edu
=====================================================
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