friedlabjhu/jwalk

A tool to calculate the solvent accessible surface distance (SASD) between crosslinked residues.

Jwalk (Python 3)

A tool to calculate the Solvent Accessible Surface Distances (SASD) between crosslinked residues

This version of Jwalk is simply a modernization of the original invented by the Topf Lab
All functionality is original and compatibility has been upgraded for Python 3
Jwalk works on Linux / MacOS / Windows

Dependencies

The following can be installed with pip

	Package
Required	BioPython
Required	numpy
Required	freesasa

Installation

  # Move to cloned directory
  cd Jwalk

  # Run install script
  python setup.py install

Running Jwalk

$ jwalk -f 1FGA.pdb Given no optional arguments, Jwalk will find all SASD between all Lys-to-Lys crosslinks in the provided PDB

Running Options

    -h, --help            show this help message and exit
    -f F                  Input path to .pdb file
    -o O                  Output path for Jwalk results (default: Out to "./Jwalk_results" in the current working
                            directory)
    -xl_list XL_LIST      OPTIONAL: Input path to crosslink list (default: Finds all Lys-to-Lys crosslinks)
    -xl_dist_cutoff XL_DIST_CUTOFF
                            OPTIONAL: Specify maximum crosslink distance cutoff in Angstroms (default: Keeps all
                            distances)
    -aa1 AA1              OPTIONAL: Specify inital crosslink amino acid three letter code (default: LYS)
    -aa2 AA2              OPTIONAL: Specify ending crosslink amino acid three letter code (default: LYS)
    -vox VOX              OPTIONAL: Specify voxel resolution to use in Angstrom (default: 1 Angstrom)
    -ncpus NCPUS          OPTIONAL: Specify number of cpus to use (default: cpu_count())

Input & Output

Crosslink lists in the -xl_list input should be pipe delmited:
res_num_1|chain_1|res_num_2|chain_2|

Example of 5 crosslinks between 2 chains:

54|A|21|B|
13|A|54|A|
2|B|13|B|
17|B|12|A|

If your PDB file does not contain chain identifiers, use "x" as the chain"

14|x|63|x|

Jwalk will create a results directory and place the outputs as follows:

./Jwalk_results
 ⎿ inputfile_crosslink_list.txt
 ⎿ inputfile_crosslinks.pdb

Visualization

To visualize the crosslinks PDB ...
In PYMOL, open the crosslinks.pdb file and set valence, 0 along with show sticks, all and hide spheres, all
In Chimera, uncomment all the MODEL lines in the PDB then open the crosslinks.pdb file and select Actions > Atoms/Bonds > show

Citation

DOI

J.Bullock, J. Schwab, K. Thalassinos, M. Topf (2016)
    The importance of non-accessible crosslinks and solvent accessible surface distance
    in modelling proteins with restraints from crosslinking mass spectrometry. 
    Molecular and Cellular Proteomics (15) pp.2491–2500

Funding

• BBSRC London Interdisciplinary Doctoral Programme (Joshua Bullock)
• MRC MR/M019292/1 (Maya Topf)

License

GPL-V3

Copyright 2016 - Josh Bullock & Birkbeck College University of London