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

                                                                                        CIF_P1(1)