Refining ligands in a structure
Hi folks, 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. Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot? 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\ 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
Joel I would suggest you update to 1.19.2 or later at http://www.phenix-online.org/download/nightly_builds.cgi
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.
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
participants (2)
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Joel Tyndall -
Nigel Moriarty