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:

To do a RCT reconstruction in EMAN2:

  1. Pick untilted/tilted particle pairs using While WEB/JWEB or DoG tiltpicker can be used, it is recommended to use ensuring that image attributes will be correct and avoiding file conversion (which can be a bit of a headache)
  2. If you are doing cryo electron-microscopy (i.e. not negative stain), CTF correct the untilted particles via phaseflipping (this improves in-plane rotation determination). Run on the untilted image stack, for example: myuntilted.hdf --voltage=300 --cs=4.1 --apix=2.1 --phaseflip --gui (of course voltage, Cs, and apix are specific to your project). Unfortuately CTF correction cannot be done, at this point, for the tilted particles because of the defocus gradient created by micrograph tilting. To remove distortion caused by the CTF, filter to the expected first zero using For example: tilted.hdf tilted_filter.hdf --process=filter.lowpass.gauss:cutoff_abs=0.05 (You might want to play around with the filtering and observe its effects on the RCT recon)
  3. Run: on the untilted particle stack. Examine the class averages, and note the rubbish ones. These will be excluded from the RCT step.
  4. Run: using the the untilted data, tilted data, class average data, stagetilt and any desired options.The untilted data used for MUST be the same as that used for the step.


To run the following 'options' are required for particles picked using --untiltedata, --tiltdata, --classavg

If you did not use to particle selection, then the following 'options' are required: --untiltedata, --tiltdata, --classavg, --stagetilt

For example: --untiltdata="bdb:RCTparticles#myuntiltedparticles" --tiltdata="bdb:RCTparticles#mytiltedparticles" --classavg="bdb:r2d_01#classes_06" --stagetilt=50 writes out a RCT reconstruction for each class average, and and averaged RCT recon if the option, --avgrcts, is activated. In addition, if the option, --align, is chosen, then the centered tilted particles will be written out. Usually these output files are written to the database.

The options are: algorithm reads in the class averages from 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

EMAN2/Programs/e2rct (last edited 2011-09-12 19:37:45 by JohnFlanagan)