NAME

       cif_cod_deposit - deposit CIFs into COD database using CGI deposition interface.

SYNOPSIS

       cif_cod_deposit --options structure1.cif structure*.cif

DESCRIPTION

       Deposit CIFs into COD database using CGI deposition interface.

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.

REPORTING BUGS

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

                                                                               CIF_COD_DEPOSIT(1)