threed_strudel (3D-Strudel)

3D-Strudel is a tool for model-dependent map-feature validation of cryo-EM structures between 2 and 4Å resolution. 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.# Sofrware requirements

OS Requirements

This package is supported for macOS and Linux. The package has been tested on the following systems:

• macOS: Monterey (12.1)
• Linux: Red Hat Enterprise Linux (7.4)

Python Dependencies

biopython
mrcfile
mpi4py
psutil
scipy

Other dependencies

• ChimeraX (1.1 < v <= 2.5)
• 3D-Strudel motif library (for map-motif validation)

Tutorials

Introduction to map-model validation with Strudel Score

Instalation

pip install threed_strudel

Setup

Set ChimeraX path

strudel_setChimeraX.py path_to_chimeraX_executable 

Get 3D-Strudel motif library

Download and unpack 3D-Strudel motif library

Usage

Map-model validation with Strudel score

strudel_mapMotifValidation.py -np nr_of_processors -p atomic_model_path -m map_path -l strudel_library_path (e.g. strudel-lib_ver-4.0_voxel-0.5/motifs_2.5-2.8) -o strudel_output_path

NOTE: for best results use the 3D-Strudel motif library resolution bin which includes the target map resolution (e.g. motifs_2.5-2.8 for a 2.6Å resolution map).

Run time: ~30 seconds per residue on a single compute core (2.9 GHz intel core i7)

To visualize the validation in ChimeraX please install the Strudel score plugin (https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore) and run:

ChimeraX --cmd 'strudel open strudel_output_path'

or

• Open ChimeraX

• On the ChimeraX command line type:

  strudel open strudel_output_path

Other

Chop an atomic model and the corresponding EM map into amino acid residues:

strudel_chopModelMapMPI.py [options]

Classify amino acid residues into rotamer classes based on the Penultimate rotamer library (JS Richardson and DC Richardson (2000) "The Penultimate Rotamer Library" Proteins: Structure Function and Genetics 40: 389-408.)

strudel_penultimateClassifier.py [options]

Superimpose and average amino acid residues maps using atom models as guide (requires rotamer classes generated by strudel_penultimateClassifier.py).

 strudel_mapAveraging.py [options]

License

threed_strudel is free and open source software released under the terms of the Apache License, Version 2.0. Source code is copyright EMBL-European Bioinformatics Institute (EMBL-EBI) 2017.