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Hi Chris, We have a script (locres.csh), available from http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/em_fitting/em_fitting.html that will calculate the local FSC for each chain in a folder of PDBs using Relion for both the mask creation and the post-processing. Best wishes, Alan On 20 May 2015, at 08:36, Sjors Scheres <[log in to unmask]> wrote: > Hi Chris, > > a. this is true: the 2 unfil.mrc will NOT be masked > b. you'll calculate a final FSC in the postprocessing program. You can > give any mask you like, and the randomized phase approach (see Chen et al > Ultramicroscopy 2013) will correct for its effects on the FSC curve. If > you let the mask cover only the best ordered bit of the map, it will be > higher than when you include the more floppy bits. This gives an > indication of local resolution, much like ResMap would. In a recenty > accepted paper on the spliceosome tri-snRNP we did this for many small > regions, and got very similar results as resmap. > Make sure your masks are always with a soft-edge, so their effects on the > FSC are not very large. It doesn't matter which program you use to make > the masks. > HTH, > Sjors > > >> Sjors and users- >> >> I am using a mask during refinements in Relion, which eliminates the small >> ribosomal subunit, thus, keeping its multiple conformations from affecting >> alignments driven by the lsu. >> I created this mask from a volume "made" in Chimera and then used >> relion_mask_create. >> >> My question is two-fold: >> >> a. The 3d half volumes made at each itr are masked by this volume, but I >> presume that the final 3d volume >> that is made when Relion converges will not be masked by this volume, is >> this correct? >> >> b. Given that part a above is true, then I presume that the final fsc >> calculated automatically in Relion will reflect the >> properties of the entire 3D volume, including the region that had been >> masked out during >> refinement, which may lower the overall resolution. >> >> While I can think of a number of ways to make a mask, what is the >> appropriate or best way to make >> a mask and the use Relion to calculate an fsc for the good region of the >> map. >> >> Of course ResMap can be used as a guide, but getting an fsc for the good >> region would be useful and >> in my reading its not clear how this is done. >> >> cheers, >> >> C Akey >> > > > -- > 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