New SWAXS calculator for atomic models

Electron density maps calculated by denss.pdb2mrc.py — Figure 5 from paper. Electron density maps of lysozyme calculated from atomic model using experimental SWAXS data. Electron density maps were calculated from the atomic model of lysozyme deposited in the SASBDB entry SASDCK8 and fitted to the experimental SWAXS data using denss.pdb2mrc.py. Density maps shown are cross sections and include (a) in vacuo, (b) excluded volume, (c) hydration shell, and (d) total (i.e., in vacuo – excluded volume + hydration shell). The density maps are colored according to density shown in the color bar in units of e-/Å3 using PyMOL.

DENSS v1.7.0 introduces a new tool for calculating highly accurate SWAXS profiles from atomic models and fitting experimental data (like CRYSOL, FoXS and others). The denss.pdb2mrc.py script will accept atomic models in the PDB format and generate a high-resolution electron density map incorporating solvent terms such as excluded volume and the hydration shell. The article describing the method has been published on Biophysical Journal (https://www.cell.com/biophysj/abstract/S0006-3495(23)00670-7), and an early draft is available on bioRxiv (https://www.biorxiv.org/content/10.1101/2023.06.02.543451v1.full).

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