Situs Flavors The Situs package includes the distribution of Situs Flavors (modified earlier versions of Situs or propotype codes for future releases). These program packages come with their own documentation and licences (if applicable) and are provided "as is" without any specific support from the biomachina team. The available Flavors include: Tomosim (Python version) can currently be found in the tomography codes, to accompany the 2021 conference paper. The dynamic programming-based map tracing codes by Salim Sazzed (Spaghetti Tracer and Struwwel Tracer) have already been included in canonical Situs. Geometric feature tracking tools, by Willy Wriggers, to accompany our paper on map and model assessment (Wriggers and He, 2015). The package shows how the data in Fig. 3 was computed. FilaSitus, by Willy Wriggers, for the creation and visualization of helical filament lattices of atomic and volumetric data. Situs 1.4, by Willy Wriggers, including the classic helical fitting tool "qhlx" and the corresponding helical fitting tutorial (for those who prefer vector quantized helical fitting inspired by the 1998 paper). Codes for Normal Mode Analysis (NMA) and Elastic Networks, by Pablo Chacón. The programs are well documented but some tools are incomplete. See the EMotion site and the 2004 review article for more information. You may also be interested in the more recent ModeHunter Python package. Alternative flexible fitting protocols for the NAMD molecular dynamics program, by Emma Falck. The routines are well documented including a nice movie of tRNA flexing with Situs and NAMD. Alternative flexible fitting protocols and tutorials for the X-PLOR refinement package, by Willy Wriggers. The X-PLOR specific tutorials are based on Situs 2.4.   Fast-Rotational Matching Codes for Alignment of 2D Images, by Yao Cong. These tools have been recently implemented in programs such as EMAN for single-particle reconstruction. Fast-Rotational Matching Codes for Alignment of 3D Objects, by Julio Kovacs. This distribution includes tools for surface matching of sphere-like objects as well as our advanced 6D search program that FFT-accelerates 5 of 6 rigid-body degrees of freedom using spherical harmonics and rotation group theory. Return to the front page .