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

 Copyright 2016 Jwalk Inventor and Birkbeck College University of London.
                      The Jwalk Inventor is: Josh Bullock


 Jwalk is available under Public Licence.
 This software is made available under GPL V3

 Please cite your use of Jwalk in published work:
 
 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

INSTALLATION: Open a terminal session and a move to the directory Jwalk is in.

type "setup.py install"

RUNNING JWALK:

Jwalk currently only runs on Unix or Linux based operating systems (sorry !)

type "jwalk" plus any of the below flags:

-h, --help show this help message and exit -lys calculate lysine crosslinks (default) -xl_list XL_LIST calculate crosslinks from input list (see Examples) -i I specify input pdb: -i <inputfile.pdb> (default runs on every .pdb in directory) -aa1 AA1 specify starting amino-acid via three letter code eg. HIS -aa2 AA2 specify starting amino-acid via three letter code eg. TYR -surface use higher accuracy method to calculate solvent accessibility - slower

if no flags are added, Jwalk will calculate the SASDs between all lysine residues on every .pdb file in the directory.

CROSSLINK LIST INPUT:

Crosslinks should be listed in a pipe-delimited .txt file as so:

res1|chain1|res2|chain2|

eg. 34|A|56|B|

If your pdb file has no chain, insert a lowercase x

eg. 34|x|56|x|

See the example file for a sample list.

OUTPUT:

Two output files are generated in ./Jwalk_results/

_crosslink_list.txt

_crosslinks.pdb

In order to visualize the crosslinks in Chimera select Actions>Atoms/Bonds>show Better representation in chimera in progress ...

Please try the test in JWalk/Examples/

Happy crosslinking !