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 untilted and tilted is at least 45 degrees, but usually 60 degrees. A larger tilt angle is desirable because RCT produces reconstructions with a missing cone, in Fourier space, a larger tilt angle reduces the cone volume. In some cases -45 and 45 degree tilt data are collected to remove the missing cone altogether. For more information see: http://www.oup.com/us/catalog/general/subject/LifeSciences/MolecularCellBiology/?view=usa&ci=9780195182187

To do a RCT reconstruction in EMAN2:

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

e2rct.py options

Where options are:

--path

string

directory that the RCT results will be placed

--untiltdata

string

The stack of untilted particle images (usually this will be in the database)

--tiltdata

string

The stack of tilted particle images (usually this will be in the database)

--classavg

string

The stack of class averages created by e2refine2d.py (usually this will be in the database)

--minproj

int

The minimum number of projections required for a RCT recon

--sym

string

RCT recon symmetry

--stagetilt

float

The angle used to tilt the stage during data collection

--careject

ints

A comma delimited list of class averages to reject

x

x

x

x

x

e2rct.py algorithm

e2rct.py reads in the class averages from e2refine2d.py and extracts the particles making up each class average. The in plane rotation for each untilted particle in each class is used in conjunction with the stage tilt, and optionally tiltaxis, to insert the tilted particle into the RCT recon, after optional centering. The net result is a RCT recon for each class average. These RCT recons are then, optionally preprocessed and aligned, and averaged.

Strategies for success