A Modified Phase-retrieval Algorithm

March 9, 2024 · View on GitHub

A modified phase-retrieval algorithm, incorporating the π-half variant of charge flipping algorithm and direct-methods tangent formula into the relaxed alternating averaged reflection phase-retrieval (RAAR) algorithm, has been developed for the determination of anomalously scattering substructures from single-wavelength anomalous diffraction (SAD) data of macromolecules.

Requirement

testting

  1. Compiling
    Edit the configure file and update the paths for fgsl/gsl, FFTW3 and CCP4 subroutine libraries in the file. Then, run:
./configure
  1. A test case, 5OQ2
    There are two inputing parameters for the modified phase-retrieval algorithm:
        (1) mtz file. This should contain the anomalous information (F+/F- or I+/I-);
        (2) 1 or 0. "1" indicates refining phases using tangent formula in the dual-space iterative cycle; "0" indicate no refinement.

The following is a case for protein with PDB entry 5OQ2:

cd exp-test/7_5oq2
./run.sh 5oq2-sf.mtz 1

The dual-space iterative framework of the Modified Phase-retrieval Algorithm

The modified phase-retrieval algorithm performs iterative dual-space recycling.The different stages are highlighted with different colors: the yellow segment signifies the algorithm’s initialization, involving the use of the random phases and experimental amplitudes to construct the initial electronic density; the blue segment encompasses reciprocal-space constraints, such as amplitude constraint, the π-half variant of charge fliping algorithm and direct-methods tangent formula; the green segment represents the direct-space constraints, including the standard RAAR algorithm and positivity constraint.

trg

Authors

  1. Geng Zhi
    Institute of High Energy Physics, Chinese Academy of Sciences (IHEP, CAS)
    Email: gengz@ihep.ac.cn
  2. Fu Xingke
    Institute of Physics, Chinese Academy of Sciences (IOP, CAS)
    Email: fuxingke0601@163.com