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: denss.fit_data.py fit a smooth curve to experimental data and calculate the corresponding P(r) (pair distribution function) includes convenient interactive GUI … [Read more...]
DENSS now part of RAW
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 … [Read more...]
UB article highlighting Nature Methods paper picked up by news outlets
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 … [Read more...]
DENSS now deals with enantiomers
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 … [Read more...]
DENSSWeb goes live
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 … [Read more...]
DENSS published in Nature Methods
The algorithm behind DENSS was published online in the high-impact journal Nature Methods. With a 5-year impact factor of 35, Nature Methods remains one of the most high-impact academic journals in the world! … [Read more...]
DENSS.org goes live
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. … [Read more...]