---
name: "cif_fix_values"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_fix_values"
---

# cif\_fix\_values(1)

correct various CIF file values and output the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from degrees Celsius to kelvins, removing temperature units of measurement, processing other undefined temperature values; - Fixing misspelled values by using the provided replacement value file; - Fixing enumeration values in CIF file against CIF dictionaries; - Correcting values of '\_exptl\_crystal\_density\_meas' data item. All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').

## NAME

cif\_fix\_values - correct various CIF file values and output the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from degrees Celsius to kelvins, removing temperature units of measurement, processing other undefined temperature values; - Fixing misspelled values by using the provided replacement value file; - Fixing enumeration values in CIF file against CIF dictionaries; - Correcting values of '\_exptl\_crystal\_density\_meas' data item. All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').

## SYNOPSIS

cif\_fix\_values --options input1.cif input\*.cif

## DESCRIPTION

Correct various CIF file values and output the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from degrees Celsius to kelvins, removing temperature units of measurement, processing other undefined temperature values; - Fixing misspelled values by using the provided replacement value file; - Fixing enumeration values in CIF file against CIF dictionaries; - Correcting values of '\_exptl\_crystal\_density\_meas' data item.

All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').

## OPTIONS

\--fix-temperature\
                   Corrects temperature values which have units specified\
                   or converts between degrees Celsius and kelvins.\
                   Changes 'room/ambiante temperature' to the appropriate\
                   numeric value. Changes other undefined values\
                   ('none', 'not given') to '?' symbol.

\--fix-misspelled replacement\_value.lst\
                   Corrects misspelled values in the CIF file. Provide a file\
                   for the check.

\--fix-dois\
                   Removes URL or DOI: prefixes from values of DOI data\
                   items.

\--fix-enums\
                   Corrects enumeration values in the CIF against CIF\
                   dictionaries. Provide dictionaries using option\
                   \--dictionaries (or -d), otherwise script uses a\
                   built-in table derived from the CIF Core dictionary.

\--treat-as-set\
                   Treats certain enumeration values as set data type in\
                   the CIF against CIF dictionaries (default). Provide\
                   dictionaries using --dictionaries (or -d) option, otherwise\
                   script uses a built-in table derived from the CIF Core\
                   dictionary.

\--fix-density-meas\
                   Corrects value of data item '\_exptl\_crystal\_density\_meas'.\
                   Values which are perceived as 'not measured' are changed\
                   to '?'. The correct units are deleted. The new data item\
                   is created if there are information about temperature.

\--fix-weighting-scheme\
                   Changes the value of the data item '\_refine\_ls\_weighting\_scheme'\
                   to the value 'calc' if it contains details which seems to\
                   have a formula, and creates new data item\
                   '\_refine\_ls\_weighting\_details' to store that information.\
                   If value is equal to number one, then it is changed to\
                   the enumeration value 'unit'.

\--fix-atom-sites-solution\
                   Corrects the most frequent mistakes in the values of\
                   data items '\_atom\_sites\_solution\_primary',\
                   '\_atom\_sites\_solution\_secondary' and\
                   '\_atom\_sites\_solution\_hydrogens'.

\-d, --dictionaries 'cif\_core.dic,cif\_cod.dic'\
                   A list of CIF dictionary files (according to DDL1)\
                   to be used in CIF file validation. List elements\
                   are separated either by ',' or by ' '. To include\
                   dictionaries with filenames containing these symbols,\
                   the --add-dictionary option is used.

\-D, --add-dictionary 'cif new dictionary.dic'\
                   Add additional CIF dictionary to the list.

\--clear-dictionaries\
                   Remove all CIF dictionaries from the list.

\--use-perl-parser

\--use-c-parser\
                   Specify parser to parse CIF files (default: C parser).

\--help, --usage\
                   Output a short usage message (this message) and exit.

\--version\
                   Output version information and exit.

## REPORTING BUGS

Report cif\_fix\_values bugs using e-mail: cod-bugs@ibt.lt