Crystallography Open Database
- COD Home
- Accessing COD Data
- Add Your Data
- Documentation
Information card for entry 2008255
Preview
| Coordinates | 2008255.cif |
|---|---|
| Original paper (by DOI) | HTML |
| Common name | paroxetine hydrochloride hemihydrate |
|---|---|
| Formula | C19 H22 Cl F N O3.5 |
| Calculated formula | C19 H22 Cl F N O3.5 |
| Title of publication | Paroxetine hydrochloride hemihydrate |
| Authors of publication | Ibers, James A. |
| Journal of publication | Acta Crystallographica Section C |
| Year of publication | 1999 |
| Journal volume | 55 |
| Journal issue | 3 |
| Pages of publication | 432 - 434 |
| a | 12.8953 ± 0.0017 Å |
| b | 10.0927 ± 0.0011 Å |
| c | 14.413 ± 0.002 Å |
| α | 90° |
| β | 106.638 ± 0.012° |
| γ | 90° |
| Cell volume | 1797.2 ± 0.4 Å3 |
| Cell temperature | 153 ± 2 K |
| Ambient diffraction temperature | 153 ± 2 K |
| Number of distinct elements | 6 |
| Space group number | 4 |
| Hermann-Mauguin space group symbol | P 1 21 1 |
| Hall space group symbol | P 2yb |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| 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. |
2008255.cif |
| 176428 | 2016-02-13 | Replaced deprecated COD CIF data names with their more modern alternatives. The _cod_cif_authors_sg_Hall and _cod_cif_authors_sg_H-M data items were renamed to _cod_original_sg_symbol_Hall and _cod_cif_authors_sg_H-M respectively. |
2008255.cif |
| 175358 | 2016-02-01 | cif/ (antanas@echidna.ibt.lt) Updating bibliography for entries 2008255, 5000135 and marking entry 5000135 as a duplicate of entry 2008255. |
2008255.cif |
| 26848 | 2011-09-28 | cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree. |
2008255.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. |
2008255.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 |
2008255.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. |
2008255.cif |
| 481 | 2008-11-20 | Changing volume number in numerous Acta Cryst. C published CIFs from 'C[0-9]?[0-9]' into '[0-9]?[0-9]'. This makes the COD CIF collection more uniform, and also helps the deposition scripts to spot potential duplicates more accurately. The command for this transformation was: for i in 2/*.cif; \ do ( \ if grep -q '_journal_volume *C' $i && \ grep -q '_journal_name_full .*Acta *Cryst' $i; \ then \ echo === $i ===; \ perl -i -pe 's/_journal_volume *C/_journal_volume /' $i; \ perl -i -pe \ "s/_journal_name_full .*/_journal_name_full 'Acta Crystallographica Section C'/" $i ; \ fi \ ) done |
2008255.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/' |
2008255.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
2008255.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. |
2008255.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) |
2008255.cif |
All data in the COD and the database itself are dedicated to the
public domain and licensed under the
CC0
License
.
Users of the data should acknowledge the original authors of the
structural data.