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Hi Yue, In the firt iteration, relion will use a normalised cros-correlation coefficient to align the particles (roughly), and then it uses its own reconstruction (which maintains greyscale). After that initial iteration, the resulting map is again filtered to whatever starting resolution you specified. HTH, Sjors > Dear Sjors, > > I was wondering how Relion converts an initial volume (e.g., produced by > EMAN2) into a new volume that shares the same absolute intensity grey > scale with experimental images during refinement. Thanks. > > Best, > Yue > -- 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