[phenixbb] Unusual ligand conformation

[Nigel Moriarty]

Joel

Can you send all files directly to me.

NB. Any files sent to me will be held in strictest confidence.

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, Mar 25, 2021 at 6:02 PM Joel Tyndall <joel.tyndall at otago.ac.nz>
wrote:

> Hi all,
>
>
>
> We have been finalising a structure with a ligand complexed to heme. I
> have been checking the close to final structure and I noticed that the
> ligand looks distorted away from what one would expect.  We use
> Phenix.refine
>
>
>
> We initially used the grade server for our restraints files. I also just
> used elbow to generate a new one. Looking at both, the restraints look
> reasonable (similar in both) however the initial output pdb from elbow is
> distorted further. The angles /lengths looked reasonable and are similar to
> small molecule structures (CCDC).
>
>
>
> The planarity of a bi-phenyl moiety is very distorted.
>
>
>
>
>
> Are we missing something?
>
> Do we need to tell phenix.refine to not over refine the model?
>
> Should elbow give a distorted model?
>
>
>
> Apologies if this is all online but my uni cant seem to access phenix.org!
>
>
>
> Thanks in advance
>
>
>
> 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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