eman - NCMI

Refine OptionsSUGGESTED (not required):●●xfiles=,, ­ Thisis a convenience option. For each 3Dmodel it will produce a corresponding x­file: threed.1a.mrc ­> x.1.mrc. Based onA/pix and mass (in kd), the x­file will bescaled so an isosurface threshold of 1will contain ~ the specified mass. 'ali to'is an iteration number. ie ­ if 'ali to' is 4,then x.7.mrc would be aligned in 3D tox.4.mrc. x.3.mrc would not be aligned atall. Often this is set to a large value, like99.3dit=, 3dit2= ­ No longersuggested. They apply a real­spaceiterative reconstruction technique to the3D model to clean up artifacts caused byFourier techniques. Typically 3dit=1 and3dit2=2. Rarely necessary, and canproduce other artifacts.●amask=,, ­ Thisoption applies an automaticallygenerated 'form fitting' soft (Gaussian)mask to the model after each iteration.The mask generation is generally quitegood. See proc3d option automask2 fordetails. This option can only be used inconjunction with xfiles=, since selectionof the threshold requires proper volumenormalization. This option can have aprofound effect on proper convergence,but should be used with caution. Tootight a mask will produce artificiallyinflated resolution values. To useproperly, insure that the mask does notcut through any significant density in thefinal model, and that the mean value isalready ~0 at the mask position. This issomewhat akin to solvent flattening.