Strudel package
Project description
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.
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