EmSartSubvolumes (cfg file)

The configuration file for reconstructing subtomograms using EmSartSubvolumes is a textfile. Individual entries are separated by newlines.

The general format is

 Parameter = Value '''\n'''

A configuration file for EmSartSubvolumes contains all entries of a EmSART configuration file and additionally the entries below.

Content

Parameter	Possible values	Description
BatchSize	Number of Particles in motivelist (limited by GPU RAM)	Number of particles to allocate memory for.
MaxShift	1-100	Maximum shift to allow during reconstruction. Can be lower than the value allowed in the refinement. If a higher value is encountered the projection in question will not be used for reconstruction of this particle.
NamingConvention	TomoParticle / nothing	Describes how subtomograms will be named based on the motivelist. TomoParticle - subtomograms will be named based on lines 5 and 6 of the motivelist, as /path/to/prefix_$(Line 5)_$(Line 6). Any other value will cause the subtomograms to be named based on line 4, as /path/to/prefix_$(Line 4).
ScaleMotivelistPosition	1	Factor to scale the motivelist rows 8, 9, and 10 (x-, y-, z-coordinates in reconstruction). For instance, 2 if working with a motivelist from a 1k reconstructiion, but a 2k reconstruction for refinement. It is recommended to refine with a motivelist of the same scale (factor = 1).
ScaleMotivelistShift	1	Factor to scale the motivelist rows 11, 12, and 13 (x-, y-, z-shifts determined by SubTomogramAverageMPI). For instance, 2 if working with a motivelist from a 1k reconstructiion, but a 2k reconstruction for refinement. It is recommended to refine with a motivelist of the same scale (factor = 1).
SizeSubVol	32 / 64 / 128 / 256 (typical boxsizes)	Box size of the reconstructed subtomograms.
VoxelSizeSubVol	1	Voxel size of the reconstructed subtomograms
SubVolPath	Location and prefix of subtomograms to be saved, e.g. "/path/to/subvol_"	Location and prefix with which to save the subtomograms.
MotiveList	Path to .em-file containing motivelist with particle positions/orientations	Motivelist containing location in original tomogram, and orientation and shift determined by SubTomogramAverageMPI for each particle.
ShiftInputFile	Location of input shiftfile created by EmSARTRefine	Path to the file containing the refined alignment for each subtomogram. In case particles should be reconstructed without a refined alignment (motivelist only), use a shiftfile of the appropriate size containing only zeros.