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Hi Qiu-Xing, Relion does not refine magnification, so you would need to rescale the images to the nearest (even) integer. It's not really recommended, but it may work. HTH, S > Dear Sjors, > I have another related question. We have two separate datasets of > different pixel sizes and collected using different detectors in the same > microscope in two separate sessions. Since Relion can take mag and pixel > size info for each particle, we would like to combine the two in one > refinement. Is this recommended? Also as we expect a small mismatch in > magnification, can Relion take it into account in its statistical model? > Thanks. > Qiu-Xing > > > On 1/18/15, 11:14 AM, "Sjors Scheres" <[log in to unmask]> wrote: > >>Dear Chia, >>The pixel size on the GUI will be internally corrected. Changing it on >> the >>GUI is not strictly necesssary, but will prevent warnings in the >>refinement runs. The important thing is that the physical detector pixel >>size in the input data.star file is now 5x larger. >>Also, if you want to re-use translations (rlnOriginX/Y) from a previous >>refinement, please be aware that those are in pixels, so you would need >> to >>divide those columns by 5. awk is a great tool for that. >>HTH, >>Sjors >> >>> Hi everyone >>> >>> I processed my unbinned data until particle extraction step. >>> Then I decide to do a binning of 5, due to the limitation of >>> computation >>> resource. >>> >>> The magnified pixel size in the GUI was 1.06 and the particle mask >>> diameter was 320. >>> so, I set Re-scaled size (pixels) in the GUI to 64. >>> >>> In order to do particle sorting, I also rescale my reference by >>> relion_image_handler with >>> "--angpix 1.06 --rescale_angpix 5.30 --new_box 64" >>> >>> My questions are: >>> 1.) am I on the right track so far ? >>> 2.) after all these steps, in the gui should I changed the The >>> magnified >>> pixel size in the GUI to 5.3 or leave it as 1.06? >>> I could do particle sorting in both cases. The two sortings look a >>> bit different but both seems ok. >>> >>> Thanks. >>> >>> Chia >>> >> >> >>-- >>Sjors Scheres >>MRC Laboratory of Molecular Biology >>Francis Crick Avenue, Cambridge Biomedical Campus >>Cambridge CB2 0QH, U.K. >>tel: +44 (0)1223 267061 >>http://www2.mrc-lmb.cam.ac.uk/groups/scheres > > > ________________________________ > > UT Southwestern > > > Medical Center > > > > The future of medicine, today. > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres