Joel

I would suggest you update to 1.19.2 or later at

 

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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