3D-Strudel

3D-Strudel is a tool for model-dependent map-feature validation of cryo-EM structures between 2 and 4Å resolution (Istrate et al., 2021). The Strudel Score is calculated as the linear correlation coefficient between the map values of a rotamer-specific map-motif from the 3D-Strudel motif library and the experimental map values around a target residue. When run from the command line, the program requires three mandatory inputs: a cryo-EM map, an atomic model, and the path to the 3D-Strudel motif library.

The validation protocol consists of the following steps:

• The map to be validated is split into individual maps, one for each residue, using model-guided segmentation (Istrate et al., 2021).
• The library motifs of each of the combined 154 rotamers of the 20 common amino acids are superimposed in turn on the map around each residue. The atomic model is used to obtain an initial superposition using the C, C𝛼 and N atoms. This superposition is then improved by map-to-map fitting, maximising the real-space correlation between the two sets of map values.
• The maximum correlation between the target residue’s local map and the map motifs for all rotamers of the same amino-acid type is reported as the Strudel score for that residue.
• For every residue, the scores with each of the rotamer motifs for the other 19 amino-acid types are also calculated. The best-matching residue type is defined as that of the rotamer with the highest correlation coefficient. If the best-matching residue type is different from the modelled residue (with a score that is more than 5% better than that of the modelled residue type), the residue is flagged as an outlier.

3D-Strudel motif library

We have mined the EMDB archive to derive map-motif libraries for all 154 rotamers of the twenty common amino acids (Lovell et al., 2000) in seven resolution bins: 2.0-2.3, 2.3-2.5, 2.5-2.8, 2.8-3.0, 3.0-3.2, 3.2-3.5, and 3.5-4.0Å. Motifs with resolution better than 2Å were not derived because of the small number of available entries in this range. We will add bins at higher resolution when more structures in this regime become available and assess the applicability of Strudel validation for such structures at that time.
The current version of the motif libraries (4.0) can be downloaded here under CC0 licence. The libraries are versioned and periodically updated.

3D-Strudel tutorial

For detailed instructions on 3D-Strudel software installation an usage please refer to the Introduction to 3D-Strudel tutorial.

Strudel Score plug-in for ChimeraX

To aid the visualisation and interpretation of 3D-Strudel results we have developed a plug-in for ChimeraX called Strudel Score. This plug-in has rich functionality to facilitate detection of possible model errors and to suggest alternative interpretations.

Software availability and installation

3D-Strudel can be obtained as part of the CCP-EM installation and it is also available from PyPI and GitHub under the Apache License Version 2.0. The Strudel Score plug-in is available from the ChimeraX toolshed and can be installed directly from within the ChimeraX program. The Strudel Score source code is available on GitHub.

Funding

This project has been funded by BBSRC (grant BB/P026893/1), the Wellcome Trust (grant 208398/Z/17/Z) and EMBL-EBI.