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
|