NAME¶

cif_p1 - expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

SYNOPSIS¶

cif_p1 --options input1.cif input*.cif

DESCRIPTION¶

Expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

OPTIONS¶

--always-continue
Continue processing and return successful return status
even if errors are diagnosed.

-c-, --always-die
Stop and return error status if errors are diagnosed.

-1, --one-datablock-output
Output all molecules and all alternative conformations
to a single output data block.

-1-, --multiple-datablocks-output
Separate each molecule and each example of an alternative
conformation into a separate data block.

-c, --covalent-sensitivity
Set a new covalent sensitivity value (default: 0.35).

--simplify-formula
Simplify chemical formula and output not the whole
P1 cell but only a minimal stoichiometric set of
molecules. Should have the same result as
'cif_molecule --preserve-stoichiometry'.

--dont-simplify-formula, --no-simplify-formula
Do not simplify formula, output the whole P1 cell (default).

--exclude-zero-occupancies
Do not use atoms with 0 occupancies in calculations
(default).

--dump-atoms
Dump atoms (including symmetry-equivalent) in CIF
format, for inspection with some graphics program.

--dont-dump-atoms, --no-dump-atoms
Do not dump atoms (default).

-i, --ignore-bumps
Detect and warn about close atom "bumps" but do not
stop processing.

--dont-ignore-bumps, --no-ignore-bumps
Stop processing immediately if bumps are detected (default).

--bump-distance-factor 0.75
A fraction of covalent bond radii sum used to determine
when atoms are too close and are considered a bump.

--max-polymer-span 4
A span, in +/- unit cells, in which polymeric molecules
(repeating units) will be constructed.

--max-polymer-atoms 100
A maximum allowed count of polymer example atoms: more
than this amount of symmetry (translational) equivalent
atoms, for each AU atom, will not be written to the output
file:

Using --max-polymer-span=0 --max-polymer-atoms=1
essentially switches off the polymer detection.

--split-disorder-groups, --dont-merge-disorder-groups
Put examples of disorder group conformations into
separate data blocks (default).

--merge-disorder-groups, --dont-split-disorder-groups
Put all disorder groups into one data block.

--use-perl-parser
Use development CIF parser written in Perl.

--use-c-parser
Use faster C/Yacc CIF parser (default).

--debug
Print some human-readable debug output.

--no-debug
Suppress any debug output (default).

--format "%8.6f"
Use the specified format for output coordinate printout.

--audit
Print audit information to the generated CIF file (default).

--no-audit
Do not print audit information to the generated CIF file.

--continue-on-errors
Do not terminate script if errors such as unrecognised
atoms are encountered; the output may be incorrect and
missing some atoms if this option is used!

--die-on-errors, --dont-continue-on-errors,

--no-continue-on-errors
Terminate script immediately if errors are raised (default).

--continue-on-warnings
Do not terminate script if warnings are raised (default).

--die-on-warnings
Terminate script immediately if warnings are raised.

--continue-on-notes
Do not terminate script if notes are raised (default).

--die-on-notes
Terminate script immediately if notes are raised.

--verbose
Print warning messages in long format.

--no-verbose
Print warning messages in concise format (default).

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

--version
Output version information and exit.

REPORTING BUGS¶

Report cif_p1 bugs using e-mail: cod-bugs@ibt.lt