/SIDESPLITTER

Primary LanguageCGNU General Public License v3.0GPL-3.0

SIDESPLITTER [ Local SNR Filter for both SIDES of SPLIT refinements ]

KAILASH RAMLAUL, COLIN PALMER, TAKANORI NAKANE & CHRISTOPHER H S AYLETT 09/06/2020

N.B. IF YOU EXPERIENCE FFTW LIBRARY ERRORS WITH THE CMAKE FILE, PLEASE

USE THE COMPILE.SH BASH SCRIPT PROVIDED - REQUIRES FFTW_DEVEL LIBRARIES

Important points:

  • SIDESPLITTER is a local SNR filter for Single Particle reconstruction
  • SIDESPLITTER is intended to maintain independence between refinements
  • SIDESPLITTER requires independent half-maps and any binary mask used
  • SIDESPLITTER outputs denoised half volumes for further alignement
  • SIDESPLITTER requires FFTW3 with POSIX threads for compilation
  • SIDESPLITTER is a C99 program (a compilation script is included)
  • SIDESPLITTER prints all its available options to stdout when called

Usage of SIDESPLITTER with RELION

  • A wrapper script is provided with SIDESPLITTER for ease of RELION use

  • The estimation of the improvment in SNR is performed by the wrapper

  • This improvement is estimated according to modification of the FSC:

    FSC_SS = (sqrt(2 (FSC + FSC^2)) + FSC) / (2 + FSC)

  • Because SNR improvement is local this can be an over or underestimate

  • If RELION refinement becomes unstable it may help to remove this

Testing and Feedback

  • SIDESPLITTER is a relatively novel technique. We believe that further validation of our method will best be facilitated by widespread use, and would actively encourage users to communicate any results from particularly difficult or interesting SIDESPLITTER refinements, especially heterogenous, conformationally flexible, poorly alignable, or contaminated datasets.
  • Novel issues, interesting outcomes, or bugs in SIDESPLITTER should be reported to the authors or CCPEM. E-mail c.aylett@imperial.ac.uk .

Installation and License

  • SIDESPLITTER is a performance optimised C program using FFTW3 Fourier transformation (Frigo and Johnson, 2005) for speed and portability
  • Compilation is easiest with CMake. Build and run SIDESPLITTER with the commands:
mkdir build && cd build
cmake ..
make
./sidesplitter

  • SIDESPLITTER is open source and is made available under the GNU public license, which should be included in any package.

    ++ Good luck & happy cryo-EM-ing - Kailash, Colin, Takanori & Chris ++