is a modular command-line-based open-source package written in C/C++ and is available under the GNU GPL License. Originally designed in 1998/9 to assist in the visualization and interpretation of cryo-electron microscopy (cryo-EM) density maps (Wriggers et al.
), its scope has been extended over the years to model multi-resolution data from a variety of biophysical sources, including tomography and small-angle X-ray scattering (SAXS; Wriggers & Chacón, 2001b
). The usefulness of hybrid multi-scale methodologies that combine atomic structures with lower resolution density maps or coarse-grained models has been well established (Mendelson & Morris, 1997
; Lindert et al.
) and the historical evolution of Situs
with application examples was reviewed in Wriggers (2010
The focus of this paper is on practical applications, specifically on workflows and conventions that are implicit to Situs programs. Over the years, owing to the modular design, the number of possible combinations of programs has increased to a point where it has become difficult to document possible workflows in our online tutorials. Based on specific modeling tasks, some new usage examples are provided here to inspire users to experiment on their own. Also, in an effort to bridge Situs to other software, many of the implicit conventions are described for the first time.
Our online tutorials (http://situs.biomachina.org
) now include Unix bash-shell scripts for the automatic generation of tutorial solutions. Much of the workflow complexity originates from the command-line-based scripting that allows programs to be combined in creative ways. Fig. 1 shows a typical example. The hypothetical problem is that one would like to bring two volumetric density maps into register. The maps can be format converted (§
2) with the map
tool or processed with ‘volume algebra’ tools (§
8) such as voledit
. For technical reasons, the rigid-body matching tools collage
require an atomic PDB file for docking to a target map (Fig. 1). Therefore, the second map must be intermittently transformed to the atomic (PDB) format using vol
so it is free from the cubic lattice (for the rotation and translation in the docking). After the matching of the pseudo-PDB map, it can be interpolated back into the volumetric format through projection onto the original lattice with pdb
Figure 1 Modular design of the Situs package. Major Situs components (blue) are classified by their functionality. The main workflow is indicated by brown arrows. The visualization (orange) for the rendering of the models requires an external molecular-graphics (more ...)
Many of the Situs
tools rely on implicit conventions for setting parameters. It is perhaps surprising to readers from the crystallographic community that important parameters of volumetric density maps such as resolution, density levels and even map formats are not strictly defined in the hybrid modeling community. For example, the surface isolevel used for visualizing a volume map is an intuitive concept that is surprisingly difficult to solve computationally. Although one can attempt to set the isolevel based on the enclosed volume (Harpaz et al.
), the resolution lowering leads to a shift in density, eroding convex features and filling up concave features of the atomic structure. To prevent convex features from protruding from the low-resolution surface, the isolevel of cryo-EM maps is empirically set to enclose 120–150% of the molecular volume depending on the overall shape of the system. This is just one example where empirical ‘fudge factors’ trump first principles. Over time, software developers have implemented conventions for a multitude of such quantities as they were breaking new ground. Although an effort is under way to standardize such conventions (Heymann et al.
), it is still often necessary to investigate the source code when sharing data between different software packages. In an effort to create more transparency, the most important Situs
conventions are documented here.
The remainder of this paper is organized as follows. §
2 describes the evolution of the Situs
and CCP4-based map formats. §
3 exemplifies the conversion between low-resolution structure types using small-angle X-ray-related bead models. §
4 contains a comparison of resolution conventions used for multi-scale biophysical data. §
5 describes conventions for coarse-grained models used in structure matching. §
6 presents correlation-based fitting approaches and the conventions used for computing the cross-correlation. §
7 presents workflows enabled by shell scripting, such as the implementation of symmetry constraints and two-dimensional projection. The paper concludes with a discussion of extended and supplemental Situs
functions in §