Crystallography Open Database

Information card for entry 9002939

Preview

Coordinates	9002939.cif
Original paper (by DOI)	HTML
External links	AMCSD

Structure parameters

Mineral name	Pyroxene-ideal
Formula	Mg O3 Si
Calculated formula	Mg O3 Si
Title of publication	Model pyroxenes I: Ideal pyroxene topologies Pyroxene #22a based on stacking sequence ABACBACBACBC Note: Atoms Mg, Si, and O are assigned to atomic positions just for convenience.
Authors of publication	Thompson, R. M.; Downs, R. T.
Journal of publication	American Mineralogist
Year of publication	2003
Journal volume	88
Pages of publication	653 - 666
a	19.5959179423 Å
b	6 Å
c	3.46410161514 Å
α	90°
β	90°
γ	90°
Cell volume	407.294 Å³
Number of distinct elements	3
Space group number	13
Hermann-Mauguin space group symbol	P 1 2/c 1
Hall space group symbol	-P 2yc
Method of determination	theoretical
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
291351 (current)	2024-04-25	Inserting Z values for entries in the 9 range, mostly missing	9002939.cif
287616	2023-11-15	cod/ (saulius@tasmanijos-velnias) Assigning AMCSD IDs to the 78 COD entries of the Thompson, R. M. & Downs, R. T. "Model pyroxenes I: Ideal pyroxene topologies" paper (DOI: https://doi.org/10.2138/am-2003-0419): 859 join -t $'\t' -1 1 -2 1 <(tail -n +3 outputs/amcsd-cod-approx-cell-updated-sg-coords-expanded.tsv \| awk '{print $2}' \| sort -u \| xargs -i bash -c 'echo -e $(cifvalues --no-data --tag _publ_section_title $(codid2file {}))"\t"{}' \| sort -u) <(tail -n +3 outputs/amcsd-cod-approx-cell-updated-sg-coords-expanded.tsv \| awk '{print $1}' \| sort -u \| xargs -i bash -c 'source functions.sh; echo -e $(cifvalues --no-data --tag _publ_section_title $(amcsd2file {}))"\t"{}' \| sort -u) \| awk -F"\t" '{print $2, $3}' \| xargs -i bash -c 'CODID=$(awk "{print \$1}" <<< "{}"); AMID=$(awk "{print \$2}" <<< "{}"); echo "_database_code_amcsd $AMID" \| (set -x; tee -a $(codid2file $CODID))' The command was run in th eworking copy of the repo: Working Copy Root Path: /home/saulius/struct/COD-crude-data URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/COD-crude-data/archives/2021/correspondence-AMCSD-COD Relative URL: ^/archives/2021/correspondence-AMCSD-COD Repository Root: svn+ssh://www.crystallography.net/home/coder/svn-repositories/COD-crude-data Repository UUID: f03e6fd5-de02-4a89-aa47-d94ad8425ebd Revision: 7455 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 7455 Last Changed Date: 2023-11-14 20:28:37 +0200 (Tue, 14 Nov 2023)	9002939.cif
183977	2016-06-27	cif/9/00/29/ Marking structures 9002907--9002987 as theoretical, adding DOIs.	9002939.cif
176465	2016-02-16	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 9.	9002939.cif
85285	2013-05-05	cod/ (saulius@koala.ibt.lt) Removing outdated _amcsd_database_code data items from all series 9 CIFs.	9002939.cif
77586	2013-03-28	cod/cif/ (saulius@koala.ibt.lt) Merging mineral data updates (_chemical_name_mineral, _chemical_name_common, structural formulae) sent to me by T.D. in his e-mail. The merge was done by the command: for i in split/*.cif do ( B=$(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)	9002939.cif
35913	2012-02-28	cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised.	9002939.cif
1210	2010-06-10	cif/9/ Updating 13213 AMCSD CIFs, taking new data from the AMCSD database and adding the assigned AMCSD numbers.	9002939.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.	9002939.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	9002939.cif
853	2009-11-16	cif/ Reconstructing spacegroup designators from the symmetry operators were possible. The comands used can be found in the log file reformat-spacegroups-2009.11.14.log committed with the current revision. Only lines that contained spacegroup designators were changed, and all files pass vcif test after the conversion.	9002939.cif
255	2008-03-10	Redepositing all AMCSD (9series) 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 &	9002939.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/'	9002939.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	9002939.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.	9002939.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)	9002939.cif