Strudel package
Project description
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
Strudel score calculation
EM map-model validation based on strudel motif libraries. Requires strudel map-motif libraries (http://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_libs/strudel-libs_ver-2.0_voxel-0.5.tar). 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]
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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