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Information card for entry 9004106
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| Coordinates | 9004106.cif |
|---|---|
| External links | AMCSD |
| Mineral name | Miserite |
|---|---|
| Formula | Ca10.54 Ce0.22 Dy0.12 Er0.06 F2 H1.34 K2.26 La0.14 Nd0.2 O46.53 Pr0.04 Si16 Tb0.1 Y1.12 |
| Calculated formula | Ca10.54 Ce0.22 Dy0.12 Er0.06 F2 H3.06 K2.26 La0.14 Nd0.2 O46.53 Pr0.04 Si16 Tb0.1 Y1.12 |
| Title of publication | Crystal structure of miserite, a Zoltai Type 5 structure |
| Authors of publication | Scott J D |
| Journal of publication | The Canadian Mineralogist |
| Year of publication | 1976 |
| Journal volume | 14 |
| Pages of publication | 515 - 528 |
| a | 10.1 Å |
| b | 16.014 Å |
| c | 7.377 Å |
| α | 96.42° |
| β | 111.15° |
| γ | 76.57° |
| Cell volume | 1081.85 Å3 |
| Number of distinct elements | 14 |
| Space group number | 2 |
| Hermann-Mauguin space group symbol | P -1 |
| Hall space group symbol | -P 1 |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 293658 (current) | 2024-08-03 | Fixing aniso label mismatch for those entries were the correspondence could be derived automatically: ( set -x; directory-metadata; cat ~/AMCSD-wrong-aniso-labels.lst.history; head ~/AMCSD-wrong-aniso-labels.lst; awk '{print $2}' ~/AMCSD-wrong-aniso-labels.lst | sort -u | xargs -i sh -c 'PERL5LIB=$(pwd)/src/lib/perl5:$PERL5LIB ./scripts/cif_fix_AMCSD_aniso_labels {} | cif_filter --add-cif-header {} | sponge {}'; date ) &> ~/cod_cif_fix_AMCSD_aniso_labels_range_9.log & The AMCSD-wrong-aniso-labels.lst was obtained from the output of the 'cif_validate' with the recent core and cod dictionaries. The 'cif_fix_AMCSD_aniso_labels' script is used from the following branch: Path: scripts/cif_fix_AMCSD_aniso_labels Name: cif_fix_AMCSD_aniso_labels Working Copy Root Path: /home/saulius/src/cod-tools URL: svn://cod.ibt.lt/cif-tools/branches/experiment/saulius-AMCSD-fix-aniso-labels/scripts/cif_fix_AMCSD_aniso_labels Relative URL: ^/branches/experiment/saulius-AMCSD-fix-aniso-labels/scripts/cif_fix_AMCSD_aniso_labels Repository Root: svn://cod.ibt.lt/cif-tools Repository UUID: 04be6746-3802-0410-999d-98508da1e98c Revision: 10202 Node Kind: file Schedule: normal Last Changed Author: saulius Last Changed Rev: 10200 Last Changed Date: 2024-08-01 17:09:44 +0300 (Thu, 01 Aug 2024) Text Last Updated: 2024-08-01 17:09:45 +0300 (Thu, 01 Aug 2024) Checksum: 566cd4f94115722d7e3512e0321a042cf7e65ab7 cif/ (saulius@tasmanijos-velnias) |
9004106.cif |
| 287555 | 2023-11-12 | cod/ (saulius@tasmanijos-velnias) Linking AMCSD entries to those COD records that had identical cell parameters, formula and bibliography, and identical atomic coordinates *after* determining atom types in AMCSD records using the 'cif_guess_AMCSD_atom_types' script from the r9700 of the ^/trunk in 'cod-tools' package repository [1]. Some COD entries matched several AMCSD entries; for those multiple related AMCSD entries were noted using the COD_RELATDE_ENTRY category, and multiple mineral names were inserted using the '_[local]_alternative_name_[]' datanames in a loop. Ref.: [1] Working Copy Root Path: /home/saulius/src/cod-tools URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/trunk Relative URL: ^/trunk Repository Root: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools Repository UUID: 04be6746-3802-0410-999d-98508da1e98c Revision: 9701 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 9701 Last Changed Date: 2023-11-12 11:14:50 +0200 (Sun, 12 Nov 2023) |
9004106.cif |
| 283907 | 2023-05-21 | cif/9/ (saulius@starta) Commiting those files that, after being processd with the new (r9581) cod-tools ^/trunk revision, have declared and calculated summary formulae differing only in hydrogen atom counts. |
9004106.cif |
| 176465 | 2016-02-16 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 9. |
9004106.cif |
| 130149 | 2015-01-27 | cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command. |
9004106.cif |
| 91987 | 2014-01-09 | cif/9/00/ (antanas@lokys) Adding _atom_site_type_symbol to prevent confusion between Wat and Wa atom types. Adding two attached hydrogens to 'Wat' atoms and one attached hydrogen to 'O-H' atoms. |
9004106.cif |
| 77586 | 2013-03-28 | cod/cif/ (saulius@koala.ibt.lt) Merging mineral data updates (_chemical_name_mineral, _chemical_name_common, structural formulae) sent to me by T.D. in his e-mail. The merge was done by the command: for i in split/*.cif do ( B=$(basename $i); C=$(echo $B|awk '{print "/home/saulius/struct/cod/cif/"substr($0,1,1)"/"substr($0,2,2)"/"substr($0,4,2)"/"$0}'); ( set -x; cif_merge --over \ _chemical_name_mineral,_chemical_name_structure_type,_chemical_name_common,_chemical_name_systematic,_chemical_formula_structural,_chemical_formula_sum \ $C $i ) \ | cif_filter --add-cif-header $C \ | sponge $C ) done in the working copy of the following repository: URL: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction/contributions Repository Root: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction Repository UUID: 9acf3947-1f02-0410-ae2a-984b57ad209b Revision: 2625 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 2625 Last Changed Date: 2013-03-28 15:13:00 +0200 (Thu, 28 Mar 2013) |
9004106.cif |
| 35913 | 2012-02-28 | cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised. |
9004106.cif |
| 966 | 2010-01-30 | cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated. |
9004106.cif |
| 858 | 2009-11-18 | cod/cif/ Changing all _chemical_formula_sum values, were necessary, to conform IUCr recommended syntax and sorting order. After this operation, it will be easier to search for structures using the _chemical_formula_sum values. Only those files and thos lines that really needed to be changed were changed; otehrwise the CIFs were not reformatted. The procedure was as follows: first, all files were passed through a 'cif_filter --parse-formula-sum' command, and the lines containing _cif_formula_sum matching tags were extracted. The extracted tags were "spliced" into the CIF files using the ./bin/{un,}grepciftag commands and awk to filter out old tags and add new tags in their place; the replacement was only done if the new tags contained "_cod_" tags ('grep -q _cod_ tmp-$$'), indicating that cif_filter has altered the formula, or the original file did not contain the _chemical_formula_sum tag ('! grep -q _chemical_formula_sum X'), indicating that cif_filter has guessed the chemical_formula_sum from the file (which should not have happened, actually). If the file was different, disregarding spaces, from the original one ('if ! diff -wb X tmp2-$$'), the original was replaced by the new file, to be committed to the repository. The full command for this step was: ( \ set -x; \ find ? -name \*.cif \ | xargs -n1 -iX \ sh -c 'cif_filter --parse-formula-sum X \ | ./bin/grepciftag _chemical_formula_sum > tmp-$$; \ if grep -q _cod_ tmp-$$ || ! grep -q _chemical_formula_sum X; \ then \ awk "/^#/,/_chemical_formula_sum/{print} /_chemical_formula_sum/{exit}" X \ | ./bin/ungrepciftag _chemical_formula_sum > tmp2-$$; \ cat tmp-$$ >> tmp2-$$; \ awk "/_chemical_formula_sum/,/\$eof/" X \ | ./bin/ungrepciftag _chemical_formula_sum >> tmp2-$$; \ if ! diff -wb X tmp2-$$; \ then \ mv -fv tmp2-$$ X; \ fi; \ fi; \ rm -f tmp-$$ tmp2-$$' \ ) >& sort-chemical-formulae-2009.11.16.log Next, the files were searched that differ from their originals only by the order of CIF tags: svn st \ | awk '/^M/{print $NF}' \ | sort | xargs -n1 -iX \ bash -c 'if diff -q <(svn cat X|sort) <(sort X) >& /dev/null; \ then echo X; \ fi' \ >& only-reordered.lst These files, after manual inspection ('cat only-reordered.lst | xargs svn diff | less'), were reverted to the originals: cat only-reordered.lst | xargs svn revert Finally, a syntax check was performed using 'vcif': svn st | awk '/^M/{print $NF}' \ | sort | xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X || { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \*.cif \ | sort \ | xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X || { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st | grep '^M' | wc -l |
9004106.cif |
| 255 | 2008-03-10 | Redepositing all AMCSD (9*series) COD CIF files. This redeposition regenerates AMCSD (9* series) files, 10011 entries total, from the original source CIF file cifdata.cif found on the CD received from Armel. Most importantly, the truncated formulas seem to be corrected. The files are not folded, i.e. they have lines longer than 80 characters (conforming CIF 1.1 specification, but not CIF 1.0 specification), and are otherwise syntactically correct. Some missing coordinates were fixed manually, restoring them from the AMCSD site, and non-ASCII symbols were fixed automatically during filtering. After the redeposition, the cifs-with-errors.lst was regenerated using the following command: find -name \*.cif \ | xargs -n1 -iI sh -c 'vcif -l 2048 I || echo I' \ | grep -vE 'CIF|ERR' \ | sort > cifs-with-errors.lst & |
9004106.cif |
| 19 | 2008-01-26 | Changing all end-of-line codes from DOS style to UNIX style in all COD CIF files, for more convenient processing: In the cod/cif/ directory: ff \*.cif | xargs perl -i -pe 's/\r\n/\n/' |
9004106.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
9004106.cif |
| 13 | 2008-01-13 | Setting the svn:keywords property to "Author Date Revision URL Id" for all CIF files in the cod/cif directory. |
9004106.cif |
| 1 | 2007-11-30 | Adding all .cif files from the COD, downloaded in a Cod.zip file on 2007.02.07 (and the same Cod.zip is downloadable today, on 2007.11.29) |
9004106.cif |
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Users of the data should acknowledge the original authors of the
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