Metadata-Version: 2.1
Name: threed-strudel
Version: 0.9.14
Summary: Strudel package
Home-page: UNKNOWN
Author: Andrei Istrate
Author-email: andrei@ebi.ac.uk
License: Apache License
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
        
        #### Map-model validation with Strudel score
        EM map-model validation based on strudel motif libraries.
        Requires [strudel map-motif libraries](https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_libs/) (e.g. [strudel-libs_ver-3.0_voxel-0.5.tar.gz](https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_libs/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](https://drive.google.com/file/d/16C2VWWnKsBnaaDd0KlX9Y0mRynPS_qdf/view)
        
            
        # 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.
            
        
Platform: UNKNOWN
Requires-Python: >=2.6
Description-Content-Type: text/markdown
