.TH CIF_COD_DEPOSIT 1
.SH NAME
cif_cod_deposit \- deposit CIFs into COD database using CGI deposition interface.

.SH SYNOPSIS
cif_cod_deposit \-\-options structure1.cif structure*.cif

.SH DESCRIPTION
Deposit CIFs into COD database using CGI deposition interface.

.SH OPTIONS
\-c, \-\-config config\-file\-with\-password.cfg
                  Specify which file holds depositor user name and
                  password. Default: "~/.cod_deposit.cfg".


\-h, \-\-host  test.crystallography.net
                  Specify the host to which the structure should be
                  deposited to.


\-p, \-\-path  cgi\-bin/cif\-deposit.pl
                  Specify script path within the host to use for structure
                  upload.


\-u, \-\-url  http://test.crystallography.net/cgi\-bin/cif\-deposit.pl
                  Specify the full URL to use for structure uploading.
                  Default: combine \-\-host and \-\-path values using
                  the "http://" protocol and "/".


\-d, \-\-deposition\-type published
                  Specify the deposition type under which the structure
                  should be deposited. Accepted values:
                  ["published", "personal", "prepublication"].
                  Default: "published".


\-s, \-\-separate\-outputs folder\-to\-put\-deposition\-outputs/
                  Specify a folder to put deposition output for each
                  deposited file.


\-r, \-\-read\-stdin
                  Read a list of CIF and Fobs file names from the standard
                  input in format
                  <CIF file> [<Fobs file> ]*
                  for example:
                  Ice.cif
                  bi5014sup1.cif all.hkl
                  bi5005sup1.cif bi50051sup2.hkl bi50052sup3.hkl


\-\-cif "input1.cif input*.cif"
                  Specify a list of CIF files to be deposited.

\-\-add\-cif "input1.cif input*.cif"
                  Specify additional CIF files to be deposited.

\-\-clear\-cif
                  Clear the list of CIF files to be deposited.


\-\-hkl, \-\-fobs
                  Specify a list of Fobs files to be deposited.

\-\-add\-hkl, \-\-add\-fobs
                  Specify additional Fobs files to be deposited.

\-\-clear\-hkl, \-\-clear\-fobs
                  Clear the list of Fobs files to be deposited.


\-\-replace
                  Specify that the given files are replacements for
                  previously deposited data.


\-\-release\-data
                  Specify that given files were previously deposited as
                  prepublication material and should be now released into
                  the public domain.


\-\-log\-message, \-\-log\-msg
                  Specify the log message for redeposited structures.


\-\-script
                  Do not deposit, print the commands to be executed
                  on deposition instead.

\-\-run
                  Enable the execution of deposition commands instead
                  of simply printing them. Default.


\-\-strict,

\-\-no\-ignore\-unpaired\-datablocks, \-\-dont\-ignore\-unpaired\-datablocks
                  Stop the deposition if any CIF data block cannot be
                  paired to any Fobs data blocks (provided that any
                  unpaired data blocks exist). Default.

\-\-silent, \-\-ignore\-unpaired\-datablocks
                  Ignore unpaired CIF and Fobs data blocks.


\-\-require\-only\-doi
                  Do not require any other bibliographic information to be
                  present if CIF data block contains resolvable DOI.

\-\-require\-full\-bibliography
                  Require all bibliographic information to be present in
                  submitted CIF file. Default.


\-\-use\-wipe
                  Use the 'wipe' command to remove temporary password
                  files. Revert to using 'rm' if 'wipe' is not available.
                  Default.

\-\-no\-use\-wipe, \-\-dont\-use\-wipe, \-\-use\-rm
                  Use the 'rm' command to remove temporary password files.
                  


\-\-common\-cif\-header
                  Use the standard COD CIF header. Default.

\-\-iucr\-cif\-header
                  Use the COD CIF header agreed with IUCr.

\-\-amcsd\-cif\-header
                  Use the COD CIF header agreed with R.D.

\-\-crystaleye\-cif\-header
                  Use the COD CIF header agreed with P.M.\-R.


\-\-print\-timestamps
                  Print timestamps to STDOUT at the start and end of
                  each CIF file deposition. Default.

\-\-no\-print\-timestamps, \-\-dont\-print\-timestamps
                  Do not print timestamps to STDOUT at the start and end
                  of each CIF file deposition.


\-P, \-\-progress
                  Ask cif\-deposit.pl to report progress of the deposition.

\-P\-, \-\-no\-progress
                  Silence cif\-deposit.pl deposition progress report messages.
                  Default.


\-\-output\-mode html
                  Specify the output mode. Accepted values:
                  ["html", "stdout"]. Default: "html".


\-D, \-\-debug
                  Request output of the progress information from
                  cif\-deposit.pl to the HTTP server log.

\-D\-, \-\-no\-debug
                  Disable the output of the progress information from
                  cif\-deposit.pl to the HTTP server log. Default.


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

\-\-version
                  Output version information and exit.

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