.TH CIF_P1 1
.SH 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).

.SH SYNOPSIS
cif_p1 \-\-options input1.cif input*.cif

.SH 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).

.SH 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.

.SH "REPORTING BUGS"
Report cif_p1 bugs using e\-mail: cod\-bugs@ibt.lt