A new chapter describing DENSS is out today in Methods in Enzymology. Written by DENSS creator Tom Grant, the chapter title "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...]
DENSS v1.6.3 updates
DENSS v 1.6.3 released today has several bug fixes and feature updates: Major/moderate updates: Updated output fit files from denss.fit_data.py to have the .fit extension common for such file types. This replaces the old *_fit.dat suffix..fit files created by denss.fit_data.py and denss.py now conform to the standard .fit format as a 4-column ascii text file containing (q, I, error, fit).When denss.py is given a file with real data and a fit, such as a GNOM .out file or the .fit file … [Read more...]
Automatic Dmax and profile fitting
DENSS v1.6.1 now includes new convenience features to automatically estimate the maximum dimension of the particle, Dmax, and perform fitting of the experimental scattering profile. denss.fit_data.py will automatically estimate Dmax when started and calculate an initial profile fit, rather than default to Dmax = 100 Ådenss.fit_data.py will now write out additional header lines to the *_fit.dat output file containing parameter values such as Dmax and Rg.denss.py now reads the header from … [Read more...]
DENSS v1.6 released
Version 1.6 contains several updates, features and bug fixes since DENSS version 1.5.0. Special thanks to Jesse Hopkins, Andrew Bruno, and Markus Meier and Fabian Heide for bug fixes and improvements. Some major updates include: GPU acceleration added (v1.5.1) (requires CuPy and CUDA GPU)Major updates to how shrink-wrap deals with negative contrast, particularly important for membrane proteins and other lipid containing particlesSeveral updates to denss.fit_data.py Some additional updates … [Read more...]
GPU acceleration with CuPy
A new --gpu option when running denss.py v1.5.1 with NVIDIA CUDA capable graphics cards is available. Tests show this option speeds DENSS up by more than 20x compared to CPU-only. Requires CuPy to be installed. We will attempt to update this in the future for more GPUs using OpenCL. Please contact us to let us know if you run into any bugs or issues. … [Read more...]
DENSS updated to Python 3
DENSS has now been updated to be compatible with both Python 2 and 3 (DENSS version 1.5+). Python 2.7 was sunset on January 1, 2020 and will no longer receive feature or security updates. To keep DENSS current and ensure compatibility with future Python updates, we have updated DENSS to Python 3. DENSS has now been tested in Python 3.6, 3.7, and 3.8 environments. DENSS is still compatible with Python 2.7 and we will attempt to maintain compatibility as long as possible. Please let us know using … [Read more...]