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Information card for entry 9003550
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| Coordinates | 9003550.cif |
|---|---|
| External links | AMCSD: 0003642, 0003646 |
| Mineral name | Carbonate-hydroxylapatite |
|---|---|
| Formula | C0.26 Ca5 O13.686 P2.829 |
| Calculated formula | C0.26 Ca5 O13.686 P2.829 |
| Title of publication | Accommodation of the carbonate ion in apatite: An FTIR and X-ray structure study of crystals synthesized at 2-4 GPa Sample: xt371 |
| Authors of publication | Fleet M E; Liu X; King P L |
| Journal of publication | American Mineralogist |
| Year of publication | 2004 |
| Journal volume | 89 |
| Pages of publication | 1422 - 1432 |
| a | 9.4803 Å |
| b | 9.4803 Å |
| c | 6.8853 Å |
| α | 90° |
| β | 90° |
| γ | 120° |
| Cell volume | 535.917 Å3 |
| Sample pressure history | synthesized at 2-4 GPa |
| Number of distinct elements | 4 |
| Space group number | 176 |
| Hermann-Mauguin space group symbol | P 63/m |
| Hall space group symbol | -P 6c |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 293656 (current) | 2024-08-03 | Correcting the AMCSD database code data name in range 9: find -name '*.cif' | xargs -i sh -xc 'perl -i -pe "s/^_amcsd_database_code/_database_code_amcsd/" {}' cif/ (saulius@starta) |
9003550.cif |
| 287548 | 2023-11-11 | cod/ (saulius@tasmanijos-velnias) Automatically adding AMCSD codes and alternative mineral names to 162 COD entries: 565 tail -n +3 outputs/amcsd-cod-exact-new-matches.tsv | awk '$NF !~ /,/ {print $3, $4}' | tr ',' ' ' | xargs -i bash -c 'ID1=$(awk "{print \$1}" <<< "{}"); ID2=$(awk "{print \$2}" <<< "{}"); CODID=$(awk "{print \$3}" <<< "{}"); source functions.sh; echo -e "_amcsd_database_code $ID1"; M1=$(cifvalues --no-dataname --tag _chemical_name_mineral $(amcsd2file $ID1)); M2=$(cifvalues --no-dataname --tag _chemical_name_mineral $(amcsd2file $ID2)); set -x; (if grep -q _cod_related_entry $(codid2file $CODID); then N=$(tail -n 1 $(codid2file $CODID) | awk "{print \$1}"); else N=0; echo -e "loop_\n_cod_related_entry_id\n_cod_related_entry_database\n_cod_related_entry_code"; fi; echo -e "$(expr $N + 1) AMCSD $ID1\n$(expr $N + 2) AMCSD $ID2"; echo -e "loop_\n_[local]_alternative_name_id\n_[local]_alternative_name_type\n_[local]_alternative_name_source\n_[local]_alternative_name_source_id\n_[local]_alternative_name_value\n1 mineral AMCSD $ID1 \"$M1\"\n2 mineral AMCSD $ID2 \"$M2\""; echo "_amcsd_database_code $ID1") | tee -a $(codid2file $CODID)'; The command was performed in the working copy: Working Copy Root Path: /home/saulius/struct/COD-crude-data URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/COD-crude-data/archives/2021/correspondence-AMCSD-COD Relative URL: ^/archives/2021/correspondence-AMCSD-COD Repository Root: svn+ssh://www.crystallography.net/home/coder/svn-repositories/COD-crude-data Repository UUID: f03e6fd5-de02-4a89-aa47-d94ad8425ebd Revision: 7437 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 7436 Last Changed Date: 2023-11-11 09:56:27 +0200 (Sat, 11 Nov 2023) |
9003550.cif |
| 283960 | 2023-05-23 | cif/9/ (saulius@tasmanijos-velnias) Estimating atom types and attached hydrogen counts for all range 9 COD entries. Atom types and hydrogen counts for about 170 entries were adjusted manually after running 'cif_guess_AMCSD_atom_types'. Commiting only those entries where declared and calculated summary formulae are matching exactly. To get the reduced formula, the Z value was estimated with 'cif_estimate_Z' after atom type adjustment. NB.: some files still do not contain the Z value, since the Z that was written into the files was estimated before the atom type correction was made, not after. The Z values will be recomputed once more after the atom types are checked in. |
9003550.cif |
| 176465 | 2016-02-16 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 9. |
9003550.cif |
| 130149 | 2015-01-27 | cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command. |
9003550.cif |
| 77586 | 2013-03-28 | cod/cif/ (saulius@koala.ibt.lt) Merging mineral data updates (_chemical_name_mineral, _chemical_name_common, structural formulae) sent to me by T.D. in his e-mail. The merge was done by the command: for i in split/*.cif do ( B=$(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) |
9003550.cif |
| 35913 | 2012-02-28 | cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised. |
9003550.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. |
9003550.cif |
| 950 | 2010-01-20 | cif/ Generating sample thermal history and and pressure history descriptions from titles or material preparation reports; to be used for distinguishing similar structures measured after different treatment. |
9003550.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 |
9003550.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 & |
9003550.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/' |
9003550.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
9003550.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. |
9003550.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) |
9003550.cif |
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Users of the data should acknowledge the original authors of the
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