[phenixbb] Restraints for small molecules in macromolecular crystal structures

[Nigel Moriarty]

Marie

The validation of ligands performed by the PDB uses Mogul. If you have
Mogul installed (free to most academic institutions, AFAIK), you can ask
eLBOW to define the bonds and angles using Mogul thus providing geometry
closer to the target. Discussions of whether this is a sound idea aside,
you can avoid many of the validation issues. Metals are always tricky so
for AD9 you may still be liaising with your annotator. I can send you a set
of Mogul restraints for AD9 if desired.

Phenix and CCP4 ship with their own restraints libraries. You can point
Phenix to the CCP4 libraries but you will remove some features from the
Phenix tools. Either way, you can load a restraints dictionary that you
have generated into Coot to do RSR etc.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909      Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Thu, Jun 10, 2021 at 6:12 AM Marie Elizabeth Fraser <frasm at ucalgary.ca>
wrote:

> Hello,
>
> The parameters we use as restraints for small molecules in complex with
> macromolecules have improved greatly, but we still get complaints when
> submitting to the Protein Data Bank. We use grade to obtain restraints for
> these small molecules, but when we submit to the PDB, some of their
> restraints do not match. I am not clear where the PDB gets these
> restraints, but we edit our file to match the values sent and finish the
> refinement.  What do others do?
>
> As well, PHENIX and COOT aren’t accessing the same library for restraints.
> Is this due to how I’ve installed ccp4 (for COOT) and PHENIX?
>
> The small molecule whose restraints I currently need is ADP metavanadate
> (AD9), which grade won’t accept because of the vanadium, so I used elbow to
> calculate restraints.
>
> Thank you,   Marie
>
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