SubTomogramAverageMPI (cfg file)

The configuration file for aligning and averaging subtomograms using SubTomogramAverageMPI is a text file. Individual entries are separated by newlines.

The general format is

 Parameter = Value '''\n'''

Conventions

1. Filenames for particles, averaged volumes (references), motivelists, and in some cases wedges are stated as prefixes terminated with an underscore. The full filenames are built on runtime based on the current iteration or information provided in the particle lists.
2. Rotations follow ZXZ convention, and are parametrized by euler angles Phi - Theta - Psi in that order.
3. Particle names are based on rows 4, or 5 and 6 of the particle list. If NamingConvention "TomoParticle" is used names are built as "/path/to/part_{row5}_{row6}.em", otherwise they're build using row 4 as "/path/to/part_{row4}.em".

Content

Parameter	Possible values	Description
CudaDeviceID	For a default 4 GPU setup: 0 1 2 3	List of the device IDs to use.
MotiveList	"/path/to/motl_"	Prefix of motivelists to be loaded/saved at each iteration.
WedgeFile	"/path/to/single_wedge.em" or "/path/to/wedge_"	Location of .em-file containing missing wedge filter or prefix of wedge-files if multiple wedges are used.
Particles	"/path/to/particle_"	Prefix of subtomograms to be loaded.
WedgeIndices	empty or "1 2 3 ..."	Indeces used to build wedge file name. Are read from motivelist(7, :) at runtime, but need to be pre-loaded here. If a single wedge file is used this should be empty.
Classes	empty or "1 2 3 ..."	Classes to include in the average. Subtomograms that have one of these numbers listed in motivelist(20, :) are included.
MultiReference	true/false	Use multi-reference mode. In this mode subtomograms are aligned to multiple references and assigned to the one with highest CCC-value. Multiple reference-prefixes need to be specified in the Reference option if "true", separated by a semicolon.
Reference	"/path/to/ref_"	Prefix of references to be loaded/saved. If multi-reference mode is used, multiple prefixes can be separated using semicolons.
Mask	"/path/to/mask.em"	Location of .em-file containing mask volume
MaskCC	"/path/to/maskCC.em"	Location of .em-file containing cc-filter for translation
NamingConvention	TomoParticle / empty	Subtomogram naming convention. If "TomoParticle", filenames are build from the from the particle-prefix and motivelist(5, :), motivelist(6, :) (i.e. Tomogram- and Particle-IDs).
StartIteration	1	The iteration number of the starting reference. I.e. for 1, "/path/to/ref_1.em" will be used.
EndIteration	2, 3, .., n	The stopping iteration. I.e. with StartIteration 1 and EndIteration 5, there will be 5 iterations run and the last generated reference will be "/path/to/ref_5.em".
AngIter	0 .. 180	Number of angular sampling points for Psi- and Theta-Angles.
AngIncr	0 .. 180	Increment between angular sampling points for Psi- and Theta-Angles.
PhiAngIter	0 .. 180	Number of angular sampling points for Phi-Angle.
PhiAngIncr	0 .. 180	Increment between angular sampling points for Phi-Angle.
LowPass	1 .. (box size/2)	Radius of spherical low-pass filter in pixels
HighPass	0 .. (box size/2)	Radius of spherical high-pass filter in pixels
Sigma	0 .. box size	Fall-off of both the high-pass and low-pass filters in pixels
ClearAngles	true/false	If true, angles are reset to the value saved in the motivelist corresponding to the value in ClearAnglesIteration after each iteration (particles are still averaged with the orientations determined in the current iteration, but this can be used to limit rotation away from an original orientation).
ClearAnglesIteration	1, 2, .., n	The iteration to be used for resetting angles.
BestParticleRatio	0 .. 1	Fraction of particles with highest CCC-value, which should be included in the average.
ApplySymmetry	true/false	See source code
CouplePhiToPsi	true/false	Couple Phi- and Psi-Angles when determining sampling.
RotateMaskCC	true/false	Rotate the maskCC-volume. Useful if it's not spherical (e.g. for membrane proteins).