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...]