Preparing PDBx/mmCIF files from Phenix/REFMAC
The best way to deposit your structure is in PDBx/mmCIF format.
Recent versions of refinement packages Phenix, REFMAC, and Buster generate PDBx/mmCIF files ready for deposition:
Phenix: Instructions are available at the Phenix website, https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html
CCP4: instructions are available for CCP4i2 (http://www.ccp4.ac.uk/deposition_ccp4i2) or CCP4 Cloud
(http://www.ccp4.ac.uk/deposition_ccp4cloud)
REFMAC (when using outside of CCP4i2 or CCP4 Cloud): To output a PDBx/mmCIF file from REFMAC, add a card that reads "pdbout format mmcif". REFMAC can also read a file by specifying a PDBx/mmCIF file as an HKLIN argument.
Buster: Instructions are available at the Buster website (https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif)
If you have have any questions about the above instructions, we suggest that you contact the authors of the
program in question.