Metadata-Version: 2.1
Name: threed-strudel
Version: 0.9.18
Summary: Strudel package
Home-page: UNKNOWN
Author: Andrei Istrate
Author-email: andrei@ebi.ac.uk
License: Apache License
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](https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_tutorials/introduction_3dstrudel/Introduction_to_3dstrudel.pdf)
        
        # 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](https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_libs/strudel-lib.4_0.5px.tar.gz)
        # 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.
            
        
Platform: UNKNOWN
Requires-Python: >=2.6
Description-Content-Type: text/markdown
