threed-strudel 0.9.13

Strudel package

threed_strudel

threed_strudel is a set of tools for cryo-EM maps data mining and motif based map-model validation.

Requirements

biopython, mrcfile, mpi4py, psutil, scipy, ChimeraX, strudel map-motif library (for map-motif validation)

Instalation

pip install threed_strudel

Set ChimeraX path

strudel_setChimeraX.py path_to_chimeraX_executable 

Usage

Map-model validation with Strudel score

EM map-model validation based on strudel motif libraries. Requires strudel map-motif libraries (e.g. strudel-libs_ver-3.0_voxel-0.5.tar.gz). The results can be visualised using the Strudel Score plugin for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore).

strudel_mapMotifValidation.py -p atomic_model_path -m map_path -l strudel_library_path (e.g. strudel-libs_ver-2.0_voxel-0.5/motifs_2.5-2.8) -o strudel_output_path

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'

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]

Tutorials

Introduction to map-model validation with Strudel Score

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.