cif_mark_disorder() | cif_mark_disorder() |
cif_mark_disorder - Marks disorder in CIF files judging by distance and occupancy.
cif_mark_disorder --options input1.cif input*.cif
Marks disorder in CIF files judging by distance and occupancy.
-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.
Report cif_mark_disorder bugs using e-mail: cod-bugs@ibt.lt