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Re: possible typos in cifdic.m95 0.7.28
Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Mon, 11 Dec 95 16:28:33 EST
Hello there -
As you all may have noticed, I usually like when I get back to work on
the dictionary to begin with the easy things to take care of - the various
typos and such that people have reported. This serves as a good warm-up
for me. So I thought I'd begin this round of changes with rsponding to
the message from Herb Bernstein about various typos that he found by
running the dictionary through CYCLOPS.
Big mistake. This turned out to be much more complicated than I had
expected, and it is thus all that I will get done today. Everything in
Herb's list (see below) has been attended to, except for the few instances
of no-longer-extant data items that are found in the audit trail (someday
soon this whole gory audit trail will go away, so we really don't need
to worry about these.)
What follows is Herb's message, and then the audit trail for the
changes I made.
Paula
Herb Bernstein writes:
> The following list was obtained by running a version of cyclops on
> cifdic.m95, version 0.7.28, and then hand editing to remove the
> data items which clearly were not typos. What remains are data
> items and line numbers which _may_ be typos. Some of these
> were reported earlier by others and some of them may already have
> been corrected in the version Paula is working on, but it seemed
> prudent to give a few too many, rather than too few.
> -- H. J. Bernstein
>
> Hand edit from:
> CYCLOPS Check List
> of cifdic.m95, 0.7.28
>
>
> Data names NOT in Dictionary Line Numbers
>
> _atom_sites.cartn_tran_matrix 3358 30799
> *** suggest _atom_sites.cartn_transf_matrix
> _chem_comp.nstd_class 6016
> *** suggest _chem_comp.mon_nstd_class
> _chem_link_bond.value_angle 7973
> *** seems to be missing definition
> _chem_link_bond.value_angle_esd 7974
> *** seems to be missing definition
> _chemical_formula.appendix 9424
> *** perhaps _chemical_formula ????
> _comp.prog.version 10113
> *** perhaps _comp_prog.version
> _comp.prog.citation_id 10114
> *** perhaps _comp_prog.citation_id
> _computing.phasing_mir 10207 19360
> *** can't find this one
> _database.code_pdb 10377
> *** can't find this one
> _diffrn.attenuator_code 12664
> *** perhaps _diffrn_attenuator.code ???
> _entity.name_com.name 14099
> *** suggest _entity_name_com.name
> _exptl.crystal_preparation 15360
> *** perhaps _exptl_crystal.preparation
> _exptl_crystal.face_ 15559
> *** perhaps _exptl_crystal_face
> _geom_bond.distance 17021 30966
> *** perhaps _geom_bond.dist
> _computing.phasing_averaging 18513
> *** could not find this one
> _computing.phasing_mad 18676
> *** could not find this one
> _refine.ls_d_res_high 22623 22639 22660 22703 22734
> 22767 22995 23029 23065
> *** could not find this one
> _refine.ls_d_res_low 22623 22639 22660 22704 22735
> 22768 22996 23030 23066
> *** could not find this one
> _refine.ls_number_reflns 22820 22869
> *** perhaps _refine.ls_number_reflns_obs
> _refine_ls_shell.reflns 23453 30739
> *** perhaps _refine_ls_shell.number_reflns_obs
> _refine.d_res_high 24333 24338 24344 24347
> *** can't find this one
> _refine.d_res_low 24334 24339 24345 24348
> *** can't find this one
> _reflns_scale_group.code 24405
> *** perhaps _reflns_scale.group_code
> _computing.save_reduction 24612
> *** can't find this one
> _reflns_shell.possible_%_obs 24987
> *** perhaps _reflns_shell.percent_possible_obs
> _struct_site_view_details 25813 25832 25851 25870 25889
> 25908 25927 25946 25965
> *** perhaps _struct_site_view
> _struct_mon.details_rscc 27214 27245 27276 27307 27630
> 27661 27692
> *** perhaps _struct_mon_details.RSCC
> _struct_mon.details_rsr 27336 27365 27394 27423 27721
> 27749 27777
> *** perhaps _struct_mon_details.RSR
> _struct_sheet.number_details 28429 28459
> *** perhaps _struct_sheet.details
> _struct_sheet_range.beg_symmetry 28889 28914
> *** perhaps _struct_sheet_range.symmetry
> _struct_sheet_range.end_symmetry 28893 28918
> *** perhaps _struct_sheet_range.symmetry
> _symmetry.equiv_pos_as_xyz 29823
> *** perhaps _symmetry_equiv.pos_as_xyz
- - - - -
+ 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
********************************************************************************
Dr. Paula M. D. Fitzgerald ______________ voice and FAX: (908) 594-5510
Merck Research Laboratories ______________ email: paula_fitzgerald@merck.com
P.O. Box 2000, Ry50-105 ______________ or bean@merck.com
Rahway, NJ 07065 USA
(for express mail use 126 E. Lincoln Ave. instead of P. O. Box 2000)
********************************************************************************