Figure 3.

Volume‐to‐pseudoatoms conversion. (a) Dialog box. (b) Superposition of an input density volume (transparent grey) and its pseudoatomic representation [spheres where the amplitudes of Gaussian functions are color‐coded from white (smallest) to red (largest)]. In this example, the Gaussian‐function standard deviation (pseudoatom radius) and the desired volume approximation error are 2 voxels and 5%, respectively. The desired volume approximation error parameter is hidden by default (“Expert Level” is set to “Normal”) and can be visualized by setting “Expert Level” to “Advanced” (panel a). The volume‐to‐pseudoatoms conversion is parallelized using threads (parallel processes sharing the same memory) and the number of threads to use can be specified in the “Threads” field (panel a). The masking options to remove background noise from the input volume are explained in the help message under the corresponding question mark (panel a)