Joel
Can you send all files directly to me.
NB. Any files sent to me will be held in strictest confidence.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
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
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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