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Hi all.. As Dr. Eleanor Dodson pointed out in the paper (Using electron-microscopy images as a model for molecular replacement, Acta Cryst (2001) D57, 1405-1409), EM density doesn't represent the presice scale of the particle. So we need to try different scales of the EM image for MR search. In addition to this scale problem, I feel I need to try different sigma levels in my case. My EM density shows more features at higher sigma-cutoff level, say 4 sigma. My case is the 3:3 complex of the two proteins which are already solved separately before. I think the density shown at 4 sigma level looks reasonable enught to accomodate all protein modules. And my EM collaborator says "The sigma level doesn't matter because it is reconstituted from negative staining. So, we can use the higher sigma level density, which is more featurous, for the atomic models to be fit in. " I don't know about the EM, but it might be the technical consequence from the negative staining. So, I want to generate a new map whose 1-sigma level density is actually the 4-sigma level density of the original one, and to get the structure factor from the new map and to try MR. But, I cannot find a way to manipulate the map in this way. Is there anybody who knows how to do it? Does this sound reasonable ? Jin Kuk Yang
