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Figure 2
Real-space fitting and visualization of SAXS bead models with Situs (Wriggers & Chacón, 2001bBB26; Wriggers, 2010BB22). (a) Atomic structure of ribonuclease inhibitor (PDB entry 1bnh; Kobe & Deisenhofer, 1996BB11). (b) Coarse-grained bead model (393 beads, 3 Å radius, hexagonal close-packed) generated from (a) with the Situs tool pdb2sax. (c) Atomic structure fitted to the bead model using collage. To show the embedded structure, the bead model is rendered as a transparent envelope. The envelope is the half-maximum isosurface of a density map created from the beads with pdb2vol using Gaussian kernel convolution with (half-maximum) kernel radius 3 Å. The images were rendered with Tachyon ray tracing using VMD (Humphrey et al., 1996BB10). For an updated review of the complete SAXS workflow, see Wriggers (2010BB22) and the SAXS tutorial at

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