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Hi Neil, If you analyse the model.star files of the subsequent iterations, do you notice anything strange? Are the scale intensity factors in the model_groups table in a reasonable range (e.g. 0.7-1.5, and not near or below 0)? Are your groups large enough after classification? HTH, S On 01/27/2014 10:53 AM, Neil Ranson wrote: > Dear All, > > I've run into a frustrating problem that I'm a bit perplexed by. > > Working on an icosahedral ssRNA virus, I did a 3D classification into 3 classes on ~22,000 particles . The classification finishes with a an indicated resolution of ~8.5Å, and two of the structures look very nice (as judged by looking at the grayscale slices through the structures. The third looks a bit ‘diffuse’. I then split the two good classes out and did an auto-refine on each. > > Here’s the problem, the first class (~12k particles) converged to a very nice structure, but the second (~6k particles) did not. Starting at a 70Å filtered starting point, the indicated resolution in each iteration went 70Å, 13.5Å, 10.5Å, 10.1Å, 11.6Å, 25.5Å, 28.3Å and then stayed there until convergence. > > Any ideas? > > KR > Neil Ranson -- 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