DENSS has been refactored to be compatible with modern Python recommendations. This allows DENSS to be on the official PyPI repository. Now DENSS can be conveniently installed with: This will automatically install the necessary packages (NumPy and SciPy) and versions to run DENSS. If you would like to automatically install matplotlib as well (for the convenient plotting options for some DENSS scripts), you can instead type: This was a fairly large refactoring of the core DENSS code. … [Read more...]
DENSS updated to v1.7.3
DENSS has been updated to v1.7.3 with bug fixes and features, including improvements in speed and robustness. DENSS has also been updated to be compatible with and integrated into BioXTAS RAW. Features and Bug fixes: … [Read more...]
New DENSS Tools in BioXTAS Raw
The latest release of BioXTAS RAW v2.3.0, a popular software package for analyzing SAXS data, now includes two new tools from DENSS, DIFT and PDB2SAS. The first tool, DIFT (DENSS IFT), uses an indirect Fourier transform (IFT) to calculate a P(r) curve from a scattering profile. DIFT is the same algorithm used by the denss.fit_data.py command line script. This algorithm has been published in Journal of Applied Crystallography (https://journals.iucr.org/j/issues/2022/05/00/vg5144/). DIFT allows … [Read more...]
New SWAXS calculator for atomic models
DENSS v1.7.0 introduces a new tool for calculating highly accurate SWAXS profiles from atomic models and fitting experimental data (like CRYSOL, FoXS and others). The denss.pdb2mrc.py script will accept atomic models in the PDB format and generate a high-resolution electron density map incorporating solvent terms such as excluded volume and the hydration shell. The article describing the method has been published on Biophysical Journal … [Read more...]
DENSS v1.7.0 released
We are excited to announce the release of DENSS v1.7.0. Included in the updates are many bug fixes, speed and stability improvements. A few new scripts have been added and updated, significant ones including denss.pdb2mrc.py and denss.mrc2sas.py. denss.pdb2mrc.py has been completely rewritten using a new algorithm to calculate electron density maps from atomic models that accurately fit experimental SWAXS data (more details in a follow up post and in our bioRxiv paper). The new script … [Read more...]
New chapter describing DENSS
A new chapter describing DENSS is out today in Methods in Enzymology. Written by DENSS creator Tom Grant, the chapter titled "Reconstruction of 3D density from solution scattering" describes in detail the DENSS algorithm, how to use the software and evaluate results, and how DENSS is unique among solution scattering modeling algorithms. The chapter includes several new figures, plots and examples with simulated and experimental data, with a particular focus on explaining how to use the software … [Read more...]
New DENSS paper for fitting SAS data
A new paper out in Journal of Applied Crystallography describes a method for fitting small angle scattering profiles with a smooth function as implemented in the denss.fit_data.py script in DENSS. The open access article, titled "Describing small angle scattering profiles by a limited set of intensities", describes in detail our approach to using an indirect Fourier transform (IFT) based on a trigonometric series (using Shannon information theory) to reduce a scattering profile to a discrete set … [Read more...]
Dihedral symmetry option added to DENSS
A new option has been added to DENSS for enforcing dihedral symmetry in addition to the previously available cyclical symmetry option. Dihedral symmetry adds n 2-fold axes of symmetry perpendicular to each cyclical symmetry related position. By applying this additional restraint for such objects, significantly improved reconstructions can be obtained. For example, many protein tetramers, rather than possessing 4-fold cyclical symmetry (C4) will instead possess D2 dihedral symmetry. Another … [Read more...]
Matters Arising articles in Nature Methods
Two new papers published today in the Matters Arising section of Nature Methods discuss the power and limitations of DENSS. Drs. Petr Konarev and Dmitri Svergun, pioneers in the field of SAXS data analysis and modeling and authors of the highly popular ATSAS package, published a Matters Arising article discussing their views on the accuracy and limitations of DENSS and its ability to reconstruct 3D density ab initio from 1D scattering profiles. As for all Matters Arising articles, I was given … [Read more...]
DENSSWeb Updated
DENSSWeb, our online web server for running the full DENSS pipeline, has recently received a major update. Try out DENSSWeb at denss.ccr.buffalo.edu DENSSWeb runs 20 individual DENSS reconstructions and aligns and averages the reconstructions. DENSSWeb now has the Fast, Slow, and Membrane modes available. Previously only Fast mode was available for quick reconstructions of simple systems, and now DENSSWeb is capable of producing results suitable for publication with the additional Slow and … [Read more...]