---
name: "cif_cod_deposit"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_cod_deposit"
---

# cif\_cod\_deposit(1)

deposit CIFs into COD database using CGI deposition interface.

## 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