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.2491โ2500
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 !