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Answer from Takanori on a query I made in relation to Beamtilt and Cs corrected microscopes. ________________________________________ From: Takanori Nakane <[log in to unmask]> Sent: 13 February 2019 12:01 To: Joseph Lyons Subject: Re: CTFrefine/beamtilt query with Cs corrected Hi, > Is the consensus not to do > beamtilt refinement on data from Cs-corrected microscopes? My short answer is yes. There is no point refining beam tilt in Cs corrected datasets (unless you are working at extremely high resolution). Phase errors due to beam tilt are proportional to Cs, as indicated in Eq. 4 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056894/. Thus, the error is very small when Cs is close to zero. The plots you attached show phase errors. As expected, your Cs-corrected dataset does not show much errors. When CtfRefine converts phase errors into a beam tilt, the values are divided by a small number of Cs, sometimes causing numerical instability and giving unnaturally large tilts. So, your large tilt (-9 mrad) is not real. Do not worry. Finally, if you don't mind, could you please forward this answer to ccpem to share it to others? Best regards, Takanori Nakane > Dear Takanori, > > > Many thanks for such a great refinement program. I am sorry to bother you > but I have a query related to CTFrefine and beamtilt refinement. I am > currently working on data from a Cs corrected Titan Krios. My query is > related to beamtilt determination on such data. Is the consensus not to do > beamtilt refinement on data from Cs-corrected microscopes? > > > Attached is a pdf of the output of CFTrefine for datasets (not the same > sample) collected on a Cs corrected and non-Cs corrected microscope. > > > The central circle in the Cs-corrected is a diffuse grey while the non-Cs > corrected data has a gradient running across this central circle. My > understanding is that the gradient indicates if beamtilt refinement is > required or not - so for the Cs-corrected data one should not do beamtilt > refinement. > > > That said the output for the Cs-corrected data give quite significant > beamtilt values for x and y compared to the non-Cs corrected data. Any > insight into why this is the case. A Cs value of 0.01 was used for the > Cs-corrected data and 2.7 for the non-Cs corrected data. > > > Regards, > > > Joe > > > ? > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1