table of contents
| cif_mark_disorder() | cif_mark_disorder() |
NAME¶
cif_mark_disorder - Marks disorder in CIF files judging by distance and occupancy.SYNOPSIS¶
cif_mark_disorder --options input1.cif input*.cifDESCRIPTION¶
Marks disorder in CIF files judging by distance and occupancy.OPTIONS¶
-d, --distance-sensitivity 0.000001 Specify maximum distance between two atoms that should be perceived as belonging to the same atom site.--occupancy-sensitivity 0.01 Set maximum deviation for the sum of occupancies of the atoms from the same atom site from 1.
-h, --add-cif-header Comments from the beginning of this file will be prepended to the output.
--exclude-zero-occupancies Do not use atoms with 0 occupancies in calculations (default).
--no-exclude-zero-occupancies
--dont-exclude-zero-occupancies Use atoms with zero (0) occupancies in the calculations.
--ignore-occupancies Do not require occupancies of the atoms in the same atom site to sum up to 1.
--no-ignore-occupancies
--dont-ignore-occupancies Require the occupancies of the atoms in the same atom site to sum up to 1 to be recognised as disorder (default).
--report-marked-disorders Print each of the marked disorder assemblies to the standard error, listing atom labels (default).
--no-report-marked-disorders
--dont-report-marked-disorders Do not print marked disorder assemblies to the standard error.
--add-depositor-comments Append reports about newly marked disorder assemblies together with the signature of this script to the '_cod_depositor_comments' value (default).
--no-add-depositor-comments
--dont-add-depositor-comments Do not append anything to the value of '_cod_depositor_comments'.
--brick-size 1 Brick size parameter for 'AtomBricks' algorithm.
--use-perl-parser Use Perl parser for CIF parsing.
--use-c-parser Use Perl & C parser for CIF parsing (default).
--help, --usage Output a short usage message (this message) and exit.
--version Output version information and exit.