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...]
DENSS v1.5 released
The major new update includes: DENSS updated to Python 3 Some additional updates include: added pdb2map_fastgauss() function which is >100x faster for calculating density from PDB atomic coordinatesfixed bugs in denss.mrcops.py related to resampling and rescalingfixed bug with origin definition when writing MRC files. Now compatible with latest versions of PyMOL … [Read more...]
New DENSS Video Tutorial
Interested in trying out DENSS? There is now a video tutorial describing the algorithm behind DENSS, how to download and install DENSS, and how to use DENSS. This video was done in collaboration with SBGRID's YouTube channel. If you use SBGRID, DENSS will be installed and available for you as part of their supported packages. To view the video, go to their YouTube page, or simply view it below: … [Read more...]
New MEMBRANE mode
DENSS now has a new mode for membrane proteins. Membrane proteins are often solubilized in detergents or lipid nanodiscs. The hydrophobic regions of these molecules often have lesser scattering density than the bulk solvent, resulting in a negative contrast relative to the solvent. The default setting for DENSS enforces a positivity restraint that will not allow any density to be negative. While this is appropriate for most standard biomolecules such as proteins and nucleic acids, is it not … [Read more...]