DENSS now includes the ability to impose symmetry to improve the resolution of reconstructions. DENSS first aligns the principal axes of the map with the x, y, and z axes. Then the value of the map at each symmetry mate location is set to the average of all related values. Imposing symmetry is as easy as setting the -ncs option. Click here to learn more.
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.
Three new scripts have been uploaded to the DENSS github repository. These scripts include: the ability to fit smooth functions to noisy experimental data (required for denss.py input), calculate scattering profiles from electron density maps, and calculate electron density maps from PDB files.
The new scripts include:
- fit a smooth curve to experimental data and calculate the corresponding P(r) (pair distribution function)
- includes convenient interactive GUI with simple sliders for selecting Dmax and the alpha smoothing factor
- calculate simple scattering profiles from MRC formatted electron density maps
- calculate simple electron density maps of arbitrary resolution from Protein Data Bank (PDB) files
DENSS has now been directly implemented within the popular RAW software package for SAXS data reduction and analysis (RAW v1.4.0). RAW contains many useful features for analyzing solution scattering data, including creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) method.
One of the main advantages to installing RAW for using DENSS, is that it DENSS is natively implemented in RAW, meaning you do not have to have a separate installation of DENSS to run it. RAW also provides a convenient graphical interface for running DENSS. For averaging, install EMAN2 and RAW will automatically find your EMAN2 installation and run the averaging procedure for you.
Many thanks to Jesse Hopkins and the RAW team for providing this for the community!
A new article by UB News reporter Ellen Goldbaum describing DENSS and the impact it will have on the scientific community was published this week. Several major scientific news outlets have picked up the article also. Read some of them here:
One of the problems with solution scattering is that enantiomers (mirror images of a particle) yield identical scattering profiles. For some particle shapes this can prove to be a serious problem resulting in opposite enantiomers being averaged during the averaging procedure. The superdenss script now includes a new option (-e) that can be used to generate all possible enantiomers for each reconstruction of denss.py and select the enantiomer that best fits the reference model. To learn how to use the option, visit the Tutorials page.
The online server DENSSWeb is now available for researchers to upload their data and perform calculations with DENSS, including full averaging with EMAN2. DENSSWeb includes an interactive viewer for visualizing the averaged electron density map in 3D using LiteMol.
DENSSWeb is also a web-based front end graphical interface that can be downloaded for personal use to perform more advanced calculations in a convenient manner, including the interactive viewer.
To use DENSSWeb, visit denss.ccr.buffalo.edu
DENSS.org is a website dedicated to the development and usage of DENSS, an algorithm for calculating electron density from solution scattering data. DENSS.org will contain the latest updates and developments and provide a central resource for the community for using the software. Instructions for installation and usage, tips, and best practices can all be found here. If you have any questions, send a message to the author below.