Crystallography Open Database

Information card for entry 5000000

4519492 << 5000000 >> 5000001

Preview

Coordinates	5000000.cif
Original IUCr paper	HTML

Structure parameters

Formula	C6 H13 N O2
Calculated formula	C6 H13 N O2
Title of publication	L-Isoleucine, Redetermination at 120 K
Authors of publication	Görbitz, Carl Henrik; Dalhus, Bjørn
Journal of publication	Acta Crystallographica Section C
Year of publication	1996
Journal volume	52
Journal issue	6
Pages of publication	1464 - 1466
a	9.681 ± 0.005 Å
b	5.301 ± 0.003 Å
c	13.956 ± 0.006 Å
α	90°
β	96.16 ± 0.04°
γ	90°
Cell volume	712.07 Å³
Number of distinct elements	4
Space group number	4
Hermann-Mauguin space group symbol	P 1 21 1
Hall space group symbol	P 2yb
Duplicate of	2004998
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
176429 (current)	2016-02-13	cif/ (antanas@kurmis) Replacing _cod_chemical_formula_sum_orig tag with _cod_original_formula_sum tag in multiple entries since the replaced tag is deprecated according to the COD CIF dictionary.	5000000.cif
176428	2016-02-13	cif/ (antanas@kurmis) Replacing _cod_cif_authors_sg_Hall tag with _cod_original_sg_symbol_Hall tag and _cod_cif_authors_sg_H-M tag with _cod_original_sg_symbol_H-M tag in multiple entries sine the replaced tags are deprecated according to the COD CIF dictionary.	5000000.cif
175228	2016-01-28	cif/5/ (antanas@echidna.ibt.lt) Adding full bibliography for entries 5000000, 5000409 and marking them as duplicates of entry 2004998.	5000000.cif
35911	2012-02-28	cif/ Reorganising ranges 1, 3, 5, 6 and 8 into a prefix-directory tree.	5000000.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.	5000000.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	5000000.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.	5000000.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/'	5000000.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	5000000.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.	5000000.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)	5000000.cif