Crystallography Open Database

Information card for entry 9005499

Preview

Coordinates	9005499.cif
Original paper (by DOI)	HTML
External links	AMCSD

Structure parameters

Mineral name	Tobermorite
Formula	Ca2.25 H7 O11 Si3
Calculated formula	Ca2.25 H5 O11 Si3
Title of publication	The real structure of tobermorite 11Å: normal and anomalous forms, OD character and polytypic modifications Note: sample MDO2
Authors of publication	Merlino, S.; Bonaccorsi, E.; Armbruster, T.
Journal of publication	European Journal of Mineralogy
Year of publication	2001
Journal volume	13
Pages of publication	577 - 590
a	6.732 ± 0.002 Å
b	7.369 ± 0.001 Å
c	22.68 ± 0.004 Å
α	90°
β	90°
γ	123.18 ± 0.01°
Cell volume	941.668 Å³
Number of distinct elements	4
Space group number	8
Hermann-Mauguin space group symbol	B 1 1 m
Hall space group symbol	B -2
Residual factor for significantly intense reflections	0.089
Diffraction radiation probe	x-ray
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
283866 (current)	2023-05-18	cif/9/ (saulius@tasmanijos-velnias) Commiting those range 9 files that, after automatic atom type determination and manual atom type and hydrogen count fixes, have declared and calculated formulae matching in all atom counts but hydrogen.	9005499.cif
282068	2023-03-26	cod/ (saulius@tasmanijos-velnias) Adding the '_cod_related_entry_...' loop to those COD AMCSD entries that lacked it, and adding the related AMCSD database ID to this loop.	9005499.cif
282053	2023-03-24	cod/ (saulius@tasmanijos-velnias) Updating the existing COD records from the recent AMCSD downloads: - Adding AMCSD IDs to those COD records that exacly matched the AMCSD structures (comparing unit cells, space groups, coordinates and measurement conditions) but did not yet have the AMCSD ID; - Adding new mineral names, compound sources, measurement conditions (when those were missing) and other informations from the AMCSD CIFs.	9005499.cif
195560	2017-04-19	cif/9/00/ Adding R(obs) and SUs for lattice parameters for entries 9005497--9005500.	9005499.cif
195559	2017-04-19	cif/9/00/ Correcting title, adding compound source and diffraction radiation details for COD entries 9005497--9005500.	9005499.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.	9005499.cif
120115	2014-07-12	Adding DOIs to range 9 structures.	9005499.cif
85285	2013-05-05	cod/ (saulius@koala.ibt.lt) Removing outdated _amcsd_database_code data items from all series 9 CIFs.	9005499.cif
35913	2012-02-28	cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised.	9005499.cif
1210	2010-06-10	cif/9/ Updating 13213 AMCSD CIFs, taking new data from the AMCSD database and adding the assigned AMCSD numbers.	9005499.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.	9005499.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	9005499.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 &	9005499.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/'	9005499.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	9005499.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.	9005499.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)	9005499.cif