Joel I would suggest you update to 1.19.2 or later at http://www.phenix-online.org/download/nightly_builds.cgi
It has been a while since we have done much with phenix. We are refining a structure with a known ligand, voriconazole (exists on the pdb). We get an error regarding a lack of .cif file/restraints.
You need to supply a restraints file (CIF format) for some ligands in Phenix.
Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot?
No not normally, only those retraints that Phenix does not have in the distributed library. Coot does not retrieve restraints, rather information.
I assume that phenix would call on a known library of ligands/monomers that are known. Is this the correct library?
phenix-installer-1.17.1-3660-intel-windows-x86_64\modules\chem_data\chemical_components\
No, this is a library of CIF files that contain information not restraints. eLBOW can create restraints from these files using the --chemical_component option. You can learn more on the Phenix Tutorials Youtube channel. www.youtube.com/c/phenixtutorials
Many thanks
Joel
Joel Tyndall | BSc(Hons) PhD
Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293 Skype: jtyndall
Website | pharmacy.otago.ac.nz
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