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...]
New symmetry averaging feature
DENSS now includes the ability to impose symmetry to improve the resolution of reconstructions. DENSS first aligns the principal axes of the map with the x, y, and z axes. Then the value of the map at each symmetry mate location is set to the average of all related values. Imposing symmetry is as easy as setting the -ncs option. Click here to learn more. … [Read more...]