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Hi, I don't think you have to worry about this. Please use a mask during refinement and apply "solvent-flattened FSC". Best regards, Takanori Nakane > Hi Takanori, > Please find my postprocess.star file attached. > Best, > Yangqi > > Sent from Mail for Windows 10 > > From: Takanori Nakane > Sent: Wednesday, August 7, 2019 12:05 PM > To: Yangqi Gu > Cc: [log in to unmask] > Subject: Re: [ccpem] Dipping in FSC > > Hi, > > Please post your postprocess.star. > > In general, some fluctuation in FSC is not uncommon in filament > processing, because of layer lines. > > Best regards, > > Takanori Nakane > >> Dear RELION developers, >> I am doing a helical refinement and noticed a warning happening once >> during the early stage of refinement (FSC dipping below 0.5 and rise >> again), although not persistent. But when I plotted the final FSC >> (unmasked), I did see a dipping around 0.5 A (although it might not >> affect >> the resolution estimate after postprocessing since the inflation caused >> the dipping at higher FSC?) I am wondering how this FSC dipping will >> affect the final map? Will it cause the wrong weighting when applying >> the >> Wiener filter (since SSNR is estimated from FSC, I assume)?I am doing a >> helical reconstruction, so I used 90% of the box size as a mask, plus a >> cylindrical mask (100 A) and the diameter of my filament is ~65 A. Is >> this >> mask still too tight? I do have some random small particles in the >> background (not ice contamination, but other proteins). Could this be >> the >> reason since the solvent is not technically flat (I tried avoid those >> particles during manual picking, but may not guarantee a total clean >> background)? >> Yangqi >> >> ######################################################################## >> >> 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