ArticleActa crystallographica. Section D, Biological crystallography2012
Conventions and workflows for using Situs.
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
117 citing papers in PubMed.
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- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
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- Mouse radial spoke 3 is a metabolic and regulatory hub in cilia.Nature structural & molecular biology · 2025Article
- Local structural flexibility drives oligomorphism in computationally designed protein assemblies.Nature structural & molecular biology · 2025Article
- The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair.Nucleic acids research · 2025Article
- ModeHunter: A Package for the Reductionist Analysis, Animation, and Application of Elastic Biomolecular Motion.The journal of physical chemistry. B · 2025Article
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- Decoys Reveal Multiple Basins of Attraction for Cryo-Electron-Microscopy Flexible Fitting.Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceedings. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.) · 2025Article
- Toward Modeling Protein Multimers by Combining AlphaFold 3 Predictions with Secondary Structures from Medium-Resolution Cryo-EM Maps.Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceedings. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.) · 2025Article
- Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation.Bioinformatics advances · 2025Article
- Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis.Nature communications · 2024Article
- Article
57 more citing papers are in PubMed but not listed here.
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Abstract
Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.
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