Hi Dan, this looks like a classic example of Fourier truncation ripples. Some relevant information: 1) Pages 19-21, 30, 32, 33 here: https://phenix-online.org/phenixwebsite_static/mainsite/files/presentations/... 2) Article "On the Fourier series truncation peaks at subatomic resolution" here: https://legacy.ccp4.ac.uk/newsletters/newsletter42.pdf 3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16Å Resolution: A. Oliver Einsle, et al. Science, 1696 (2002) 297 4) Page 267 Figure 4: On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev Acta Cryst. (2004). D60, 260-274 Check refined parameters of involved atoms -- occupancy, B, coordinates. Use adequate map contouring levels -- for sufficiently low contouring levels you're likely to see something like this for most atoms in most atomic models just because this is an inherent property of a finite resolution Fourier image of electron density distribution. Good luck! Pavel On 2/9/26 06:00, Dan Richman via phenixbb wrote:
Hi Phenix folks,
Have any crystallographers seen the phenomenon I've captured in these screenshots (linked below to save space), of concentric, semi-spherical, alternating layers of difference density? It seems to be localized at a valine side chain at the edge of the model and reflected across some two-fold symmetry. There's no heavy metal in the crystallization.
Overall, the quality of the map and the model refinements are very good; everything has behaved as expected. We're just trying to diagnose this phenomenon and our searches for related descriptions have not yielded anything.
Thanks!
-- Dan Richman, PhD (he/him/his) Research Associate, James Berger Lab Dept of Biophysics and Biophysical Chemistry Johns Hopkins University School of Medicine mobile: 201-669-0967 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s