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| '''I have processed my data set to high resolution, but I'm sure the raw data is heterogeneous. Is there any way for me to resolve this heterogeneity to get a better resolution structure out, or to produce multiple models from my single data set ? ''' Two approaches have evolved in EMAN for dealing with heterogeneous data sets. * The 'mutlirefine' program has syntax almost identical to the 'refine' command, but it simultaneously refines several 3-D reconstructions from a single input data set. Generally the best results are achieved when the particles going into each model produced by multirefine are further refined independently. That is generally accomplished like this: * Run multirefine ... for several iterations. Don't interrupt it, but allow it to complete the last specified iteration. * then, from the root mulirefine directory (shell script for zsh, but you get the drift: {{{ mkdir r0 r1 cd 0 foreach i (cls*lst) proc2d $i ../r0/start.hed first=1 end cp threed.4a.mrc ../r0/threed.0a.mrc (use the last iteration) cd ../1 foreach i (cls*lst) proc2d $i ../r1/start.hed first=1 end cd ../r0 refine ... cd ../r1 refine ...}}} * Run refine2d.py (use EMAN 1.8 or newer) on start.hed without the finalsep option. When it completes, use (zsh script) {{{ foreach i (cls*lst) proc2d $i avgs.hed average end}}} Then either manually, or using multirefine (on avgs.hed), separate the data you want from avgs.hed. For each image in avgs.hed that you want to keep, you could run: {{{ proc2d cls0023.lst mygooddata.hed }}} The problem with this is that, while you would get the particles you want, they are already aligned in 2-D to the class-average. If you used these particles for futher processing, they would end up getting rotated a second time, which may adversely effect your final resolution, so instead, run: {{{ ~/EMAN/python/lstsub.py cls0023.lst mygooddata.hed ptcl2orig.lst }}} This will copy the original unrotated particles corresponding to each class. Once you have the particles you want in mygooddata.hed, you can run refine or other postprocessing on it. |
I have a heterogeneous data set and want to know where I can find information on the phase residuals of the data set in EMAN to see if it can reveal the extent of the heterogeneity of my data. |
I have a heterogeneous data set and want to know where I can find information on the phase residuals of the data set in EMAN to see if it can reveal the extent of the heterogeneity of my data.