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 Å
• denss.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 *_fit.dat files, removing the need to explicitly set the -d option
• if no Dmax is given to denss.py, Dmax will be automatically estimated from the data
• if raw experimental data are given to denss.py, rather than the expected smoothed/fitted profile, Dmax will be estimated from the experimental data and the data will be fitted with a smooth profile. It is still recommended to manually run denss.fit_data.py first to ensure accurate fitting and Dmax estimation.

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 particles
• Several updates to denss.fit_data.py

Some additional updates include:

• fixed bugs in denss.all.py with writing log files, added FSC curve plotting and made filenaming consistent with superdenss
• bug fixes to maintain compatibility with BioXTAS RAW
• denss.fit_data.py updates:
  • residuals plot shares x-axis of intensity plot
  • added text boxes for explicit input of Dmax, alpha
  • slider limits automatically update as values get close to the edges of the slider
  • can trim data in the GUI, removing first and/or last data points
  • P(r) function now written out to file
• fixed bug in denss.rho2dat.py where negative values were set to zero by default
• added option to denss.refine.py to add simple uniform noise to starting density
• new pdb2mrc_multigauss() function for quickly and accurately calculating density from atomic coordinates. This function uses a fast and accurate 5-term Gaussian summation in real space using Cromer-Mann coefficients for the atomic form factors. Users can access this feature with the denss.pdb2mrc.py script.
• fixed bugs when reading/writing large PDB files. Added ability to ignore waters when reading PDB files and remove atoms.
• changed alignment score to -correlation instead of 1/correlation.
• removed separate unnecessary translation step in density alignment to reduce interpolation artifacts
• updates to shrink-wrap:
  • to improve reconstructions with negative contrast, shrink-wrap was updated to utilize two separate shrink-wrap modes: shrinkwrap_by_density (the standard version) and a new shrinkwrap_by_volume function. The volume-based version will select N voxels with the highest density (of the blurred map), where N is chosen to satisfy a desired volume. This is in contrast to the standard version which selects voxels based on a fixed threshold. Now shrink-wrap will first be based on volume, and then switch to the standard threshold-based version.
  • the “sigma” parameter, defining the width of the Gaussian filter used for blurring, is now based on physical distance, rather than number of voxels. Previously, if a reconstruction used a higher resolution, the voxel sizes would be smaller, and thus the blurring would be less, resulting in greater noise in the reconstructions. This update fixes this issue.
  • default sigma values for membrane mode is now two times the standard values
  • new “erosion” step included in membrane mode to remove artifactual negative density at edges of positive density
  • new –sw_old option available for users who prefer the old version of shrink-wrap
  • recentering during shrink-wrap now only occurs if recenter option is set
• fixed bug in denss.mrcops.py when converting from electrons to density

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.

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 coordinates
• fixed bugs in denss.mrcops.py related to resampling and rescaling
• fixed bug with origin definition when writing MRC files. Now compatible with latest versions of PyMOL