DENSS

DENsity from Solution Scattering

  • About DENSS
  • Download
  • Install
  • Tutorial
    • Introduction
    • Basic Usage
    • Averaging with DENSS
    • Averaging with EMAN2
    • Advanced Usage
    • Tips
  • News

New SWAXS calculator for atomic models

June 23, 2023 by Tom Grant

Electron density maps calculated by denss.pdb2mrc.py

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 is available on bioRxiv (https://www.biorxiv.org/content/10.1101/2023.06.02.543451v1.full). … [Read more...]

Filed Under: Developments, News

DENSS v1.7.0 released

June 23, 2023 by Tom Grant

Plot of the fit of a DENSS map to experimental data

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...]

Filed Under: Developments, News

New chapter describing DENSS

November 4, 2022 by Tom Grant

DENSS reconstruction of GLIC membrane protein from SANS data

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...]

Filed Under: News

New DENSS paper for fitting SAS data

October 4, 2022 by Tom Grant

Bn functions for SAS fitting

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...]

Filed Under: News

Dihedral symmetry option added to DENSS

March 24, 2021 by Tom Grant

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...]

Filed Under: Developments, News

Matters Arising articles in Nature Methods

March 1, 2021 by Tom Grant

DENSS accurately reconstructs density from SAXS

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...]

Filed Under: News

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Contact the Author:

  • Email
    tdgrant@buffalo.edu
  • Phone
    (716) 829-5490
  • Address
    Jacobs School of Medicine and Biomedical Sciences
    SUNY University at Buffalo
    955 Main Street
    Buffalo, New York, USA 14203

Contact the Author:

  • Email
    tdgrant@buffalo.edu
  • Phone
    (716) 829-5490
  • Address
    Jacobs School of Medicine and Biomedical Sciences
    SUNY University at Buffalo
    955 Main Street
    Buffalo, New York, USA 14203

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