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...]

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...]

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...]

DENSS now has a new built-in averaging procedure since v1.4.4. The alignment works by first performing a coarse-grained rotational search uniformly sampled around a sphere to find the best coarse alignment. Then a fine alignment is performed using minimization including rotational and translational degrees of freedom. Enantiomer generation and selection is included, as well as the use of a binary tree algorithm for creating a reference volume for alignment. Previously averaging was dependent … [Read more...]

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...]

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...]