Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
By Grigore D. Pintilie, Junjie Zhang, Thomas D. Goddard, Wah Chiu, D. Gossard. Journal of Structural Biology, 2010
399 citations recorded by the source corpus.
Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the immersive watershed method and grouping of the resulting regions using progressively smoothed maps. The method requires only three parameters: the segmentation threshold, a smoothing step size, and the number of smoothing steps. We first apply the method to maps generated from molecular structures and use a quantitative metric to measure the segmentation accuracy. The method does not attain perfect accuracy, however it produces single or small groups of regions that roughly match individual proteins or subunits. We also present two methods for fitting of structures into density maps, based on aligning the structures with single or groups of regions. The first method aligns centers and principal axes, whereas the second aligns centers and then rotates the structure to find the best fit. We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally obtained density maps.
Subfields: Radiation, Structural Biology, Surfaces, Coatings and Films
View Paper: https://www.semanticscholar.org/paper/0be5baf0370578430d94eeccdbdccb4887453f50
How researchers see this paper
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In Structural Biology
- Thomas D. Goddard
- Wah Chiu
- Jianlin Lei
- Dina Schneidman-Duhovny
- Sjors H. W. Scheres
- M. A. Tortorici
- D. Veesler
- A. Walls
In Surfaces, Coatings and Films
Citations in the corpus
- Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking (2012, methodology): “Several semi-automated tools, such as EMAN2’s e2segment3d.py (Tang et al., 2007) and Segger (Pintilie et al., 2010), are available to segment out the density.”
- Molecular Architecture of the SARS-CoV-2 Virus (2020, positive): “One segment above and two on the base forming a reverse ‘‘L’’ from the best solved region were selected, and were fitted with a N_CTD dimer (6WJI) using the ‘fit to segments’ tool (Pintilie et al., 2010) in UCSF Chimera.”
- UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “These capabilities augment over 100 tools already provided by Chimera for the interactive analysis of atomic models, density maps, and protein sequences (Couch et al., 2006; Goddard et al., 2005, 2007; Meng et al., 2006; Morris et al., 2007; Pettersen et al., 2004; Pintilie et al., 2010).”