DENSS now has a new built-in averaging procedure since v1.4.4. The alignment works by first performing a coarse-grained rotational search uniformly sampled around a sphere to find the best coarse alignment. Then a fine alignment is performed using minimization including rotational and translational degrees of freedom. Enantiomer generation and selection is included, as well as the use of a binary tree algorithm for creating a reference volume for alignment.
Previously averaging was dependent on the installation of EMAN2, a powerful suite of tools primarily designed for reconstructing electron microscopy volumes. However, EMAN2 is a large package and DENSS only uses a small part of that package. Our new built-in procedure was made partially to alleviate this dependency.
This update contains a host of new scripts for performing various tasks. The primary script for performing multiple runs of DENSS and averaging the results is denss.all.py. Additional scripts enable alignment of maps to models, calculation of resolution, and even a new refinement script. For a full list of the new scripts and tutorials on how to use them, click here.
The new averaging procedure has been tested and works on Windows as well. The popular RAW SAS data processing package contains the new averaging procedure as well as of RAW v5.0.
Thanks to Nhan Nguyen for his help writing much of the code.