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When the <prefix>/share/libcifpp directory contains a components.cif.gz, but not a components.cif, I get the following error runnig mkdssp:
Configuration error:
The attempt to retrieve compound information for "GLN" failed.
This information is searched for in a CCD file called components.cif or
components.cif.gz which should be located in one of the following directories:
"<prefix>/share/libcifpp"
"<prefix>/share/libcifpp"
"<prefix>/share/libcifpp"
(Note that you can add a directory to the search paths by setting the
LIBCIFPP_DATA_DIR environmental variable)
On Linux an optional cron script might have been installed that automatically updates
components.cif and mmCIF dictionary files. This script only works when the file
libcifpp.conf contains an uncommented line with the text:
update=true
If you do not have a working cron script, you can manually update the files
in /var/cache/libcifpp using the following commands:
curl -o<prefix>/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
curl -o <prefix>/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
curl -o <prefix>/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic
No compound factory objects are created since none of the data sources is found.
Unknown compound: GLN
Unknown compound: ALA
Unknown compound: ASP
...
The error message claims "This information is searched for in a CCD file called components.cif or
components.cif.gz", but the compressed components.cif.gz exists in the share directory:
$ ls <prefix>/share/libcifpp/components.cif.gz
components.cif.gz dssp-extension.dic mmcif_ma.dic mmcif_pdbx.dic mmcif_pdbx_v50.dic
Unpacking the components.cif.gz into components.cif makes mkdssp work again.
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