Rhys
You can use the phil option
superpose_ideal_ligand = *None all SF4 F3S DVT
to superpose an ideal F3S to avoid the mess. I'm also happy to take a
closer look.
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 : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Mon, Apr 18, 2022 at 11:50 AM Edward Berry
Have you seen: Iron–sulfur clusters have no right angles Nigel W. Moriarty and Paul D. Adams, Acta Cryst. (2019). D75, 16–20 http://journals.iucr.org/d/issues/2019/01/00/rr5165/index.html
The Phenix F3S library worked well for our Complex II structures a few years back. And those structures definitely confirm that the angles are not 90* for F3S. (FES Fe2S2 has close to right angles, I think) You have to be sure that the atoms are arranged in the same way as in the model or the restraints will try to invert your cluster;, and that the Cys ligands connect to the right irons. Ed
Hi PHENIX BB,
I'm currently refining a structure with 3Fe4S clusters into some high resolution cryoEM maps (1.57 Ang). However, refinement messes up the Fe4S cluster, by moving the existing Fe and S atoms into the wrong positions in
Rhys Grinter wrote on 4/18/2022 12:24 AM: the density.
Is anyone aware of this issue and/or knows of a simple way to prevent
this from happening?
Cheers,
Rhys
-- Dr Rhys Grinter Lab Head Molecular Physiology of Microbial Pathogens (MP2) Lab Monash University +61 (0)3 9902 9213 +61 (0)403 896 767
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