[phenixbb] Refining ligands in a structure

[Nigel Moriarty]

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
>
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>
> 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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