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Dear Joshua, The absolute greyscale of the SPIDER classes is probably not maintained correctly, and therefore the picking goes all wrong. If that's the case, you cannot use those classes in relion. HTH, S > Hi All I have run upto the autopicking stage in relion 1.3 using the > steps detailed in the Relion 1.3 manual and was also able to run the > autopick program successfully.However I was not happy with the particles > that the program picked > I was wondering if it was possible to introduce 2D averages which were > obtained from an external program like SPIDER. The 2D averages I have > would serve as a better reference to help the autopick program if it can > be done. I tried autopicking with the SPIDER references and found that the > autopick did not pick any particles but ran successfully.I am dealing with > noisy cryo EM data. thank you for you time . Sincerely Joshua Lobo -- 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