Crystallography Open Database

Information card for entry 1100066

1100065 << 1100066 >> 1100067

Preview

Coordinates	1100066.cif

Structure parameters

Common name	hydroxylapatite
Formula	?
Calculated formula	Ca8 O28 P6
Title of publication	Al2O3 - ZrO2 standard
a	9.048 ± 0.001 Å
b	9.047673 Å
c	6.704 ± 0.001 Å
α	90°
β	90°
γ	120°
Cell volume	475.29 Å³
Number of distinct elements	3
Hermann-Mauguin space group symbol	P63/m
Residual factor for all reflections	0.696051
Weighted residual factors for all reflections	0.505776
Goodness-of-fit parameter for all reflections	0.717446
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
130149 (current)	2015-01-27	cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command.	1100066.cif
77888	2013-03-29	cod/ (saulius@koala.ibt.lt) Merging Luca's changes to two CIFs.	1100066.cif
77587	2013-03-28	cif/ (saulius@koala.ibt.lt) Removing the 'Phase unknown' lines from two range 1 entries.	1100066.cif
35911	2012-02-28	cif/ Reorganising ranges 1, 3, 5, 6 and 8 into a prefix-directory tree.	1100066.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.	1100066.cif
900	2009-11-21	cif/ Renaming data blocks of all COD CIFs so that they have COD number (taken from the COD file name) as their datablock number: find ? -name \.cif \ \| xargs \ perl \ -MFile::Basename \ -i \ -lpe 's/^data_([^\s])/"data_".basename($ARGV, ".cif")/e' After this change, 'cif2cod' will give correct keys in the generated table. Also, data block names are guaranteed to be distinct, so any subset of COD CIFs can be concatenated into one file without introducing ambiguity.	1100066.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	1100066.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/'	1100066.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	1100066.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.	1100066.cif
10	2008-01-04	BUG FIX: renaming all CIF files that had extension with all capital letters (.CIF) into files written in all lowercase (.cif). On Linux, where filenames are strictly cae-sensitive, the Web site engine would not find files that had .CIF extension (written in all caps).	1100066.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)	1100066.cif