Reconstruction via Random Conical Tilt (RCT)

In EMAN2 an initial model can be constructed using RCT and a stack of untilted and tilted particles whose set element relationship is on-to-one. Typically the tilt angle between the unilted and tilted is at least 45 degrees, but usually 60 degrees. A larger tilt angle is desireable because RCT produced reconstructions with a missing cone, in Fourier space, and a larger tilt angle reduces the cone volume. In some cases -45 and 45 degree tilt data are collected to remove the missing cone alltogether. To do a RCT reconstruction in EMAN2:

Pick untilted/tilted particle pairs using e2RCTboxer.py. While WEB/JWEB or DoG tiltpicker can be used, it is recommended to use e2RCTboxer.py because that ensures that image attributes will be correct and avoids file conversion (which can be a bit of a headache)
Run: e2refine2d.py on the untilted particel stack. Examine the class averages, and note the bas ones. These will be excluded from the rct step.
Run: e2rct.py using the data and options described below.

e2rct.py options

Where options are:

--path: directory that the RCT results will be placed
--untiltdata: The stack of untiltedparticle images (usually this will be in the database)
--tiltdata: The stack of tilted particle images (usually this will be in the database)
--classavg: The stack of classaverages created by e2refine2d.py (usually this will be in the database)
--minproj: The minimun number of projections required for a RCT recon
--sym: RCT recon symmetry
--stagetilt: The angle used to tilt the stage during data collection
--careject: A comma delimted list of class averages to reject
--align: Center the tilted images before RCT reconstruction (impoves recon quality) (Boolean toggle switch)
--maxshift: Maximum to shift the tilted images during centering (Boolean toggle switch)
--tiltaxis: Do a per micrograph tilt axis correction, which improves qualiyt if there is a large tiltaxis variation. (only works for e2RCTboxer.py data) (Boolean toggle switch)
--avgrcts: Align3D and average the each of the RCT recons, from each classaverage (Boolean toggle switch)
--alignran: Finess of 3D alignment search
--wieghtrecons: During averaging weight the RCT recons by number of tilted images used to create each one
--verbose: Set the verbosity level