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Dear Takanori, Thank you for your advice. With "--ewald --reverse_curvature" and without "--ewald", relion_reconstruct gave the same resolution estimate. Only relion_reconstruct --ewald showed a poorer estimate. I do not understand this behavior, but I agree that Ewald sphere correction is not so significant in my case as you pointed out. Thank you so much again. Best regards. Tasuku On 2018/10/26 19:58, Takanori Nakane wrote: > Hi, > > What resolution do you get if you run relion_reconstruct > without --ewald? The difference between this value and Refine3D > reflects the effect of marginalisation. > The difference is usually tiny but your case might be an exception. > > Also, according to the formula in > https://www.ncbi.nlm.nih.gov/pubmed/16384646, > the effect of Ewald sphere curvature for a 300 A particle should be > very small at ~ 2.9 A. > > Best regards, > > Takanori Nakane > >> Dear all, >> >> I obtained a 3D structure of a spherical virus with a diameter of about >> 300 A by RELION-3 beta. >> 3D auto refine and postprocess produced a 2.88 A resolution map. >> >> Then, I tried relion_reconstruct --ewald with and without >> --reverse_curvature as, >> >> relion_reconstruct --i Refine3D/job172/run_data.star --o >> reverse_half1.mrc --subset 1 --angpix 1.24 --ctf --ewald --mask_diameter >> 400 --sectors 2 --width_mask_edge 5 --sym I1 --reverse_curvature >> >> Here Refine3D/job172/run_data.star is output from 3D auto refine. >> >> Postprocessing the resulting maps showed 2.91A and 3.05A resolutions >> with and without --reverse_curvature, respectively. >> >> So I think Ewald sphere correction is effective, but the resolution by >> relion_reconstruct --ewald is lower than by auto refine (with no Ewald >> sphere correction). >> I wonder if there is a way to improve the resolution of the original 3D >> auto-refined map (2.88 A resolution) by Ewald sphere correction. >> >> Thank you in advance, >> Best regards, >> >> Tasuku >> >> ######################################################################## >> >> To unsubscribe from the CCPEM list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >> > ######################################################################## > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1