<> = e2pathwalker.py = e2pathwalker.py is a component of [[Pathwalker]], described in the following publication: * [[http://www.sciencedirect.com/science/article/pii/S1047847716301101 | Chen, M., Baldwin, P.R., Ludtke, S.J., Baker, M.L., 2016. De Novo Modeling in Cryo-EM Density Maps with Pathwalking. Journal of Structural Biology]] * [[http://www.ncbi.nlm.nih.gov/pubmed/22405004|Baker, M.R., Rees, I., Ludtke, S.J., Chiu, W., Baker, M.L., 2012. Constructing and validating initial cα models from subnanometer resolution density maps with pathwalking. Structure 20, 450-463.]] = Installing a TSP Solver = e2pathwalker.py is included in the EMAN2 distribution, but requires a third party Traveling Salesman Problem (TSP) solver to run. Two TSP solvers are supported: LKH and Concorde. == Installing LKH == We generally use LKH as the TSP solver for Pathwalker; it is fast, works well, and is relatively easy to compile. You can download LKH from the author's site: * http://www.akira.ruc.dk/~keld/research/LKH/ It is pretty easy to compile -- go into the LKH-2.0.5/SRC directory and run "make". This will result in a binary "LKH" in LKH-2.0.5. You can copy this to /usr/local/bin or somewhere in your $PATH. == Installing Concorde == ... = Running Pathwalker = e2pathwalker.py operates on a single PDB file. With no additional options, it will simply read the PDB file and print out some statistics. To actually run the TSP solver, use the --solve option, with either --solve=lkh to use the LKH solver, or --solve=concorde to use the Concorde solver. To save the TSP results, use the --output option with a filename: e.g. --output=test.pdb By default, e2pathwalker.py will use the 'CA' atoms in 'A' chain in the input file; this can be changed with the --atomtype and --chain options. There are several additional options; the current e2pathwalker.py options can be displayed using --help. {{{ muta:~ irees$ e2pathwalker.py --help usage: e2pathwalker.py [options] Find paths between two atoms in a PDB model. You can also specify two PDB files to calculate an RMSD. Use "--solve=" to run the TSP solver and save the output. Use "--output" to save the output to a PDB file. Pathwalker wiki: http://blake.bcm.edu/emanwiki/Pathwalker positional arguments: postionalargs optional arguments: -h, --help show this help message and exit --version show program's version number and exit --output OUTPUT Output file --start START Start ATOM --end END End ATOM --average AVERAGE Average Ca-Ca length --dmin DMIN Mininum Ca-Ca length --dmax DMAX Maximum Ca-Ca length --noise NOISE Add Gaussian Noise --solver SOLVER Run TSP Solver: concorde or lkh --atomtype ATOMTYPE Load Atom Type. Default: 'CA'. Options: 'C' or 'all' --chain CHAIN Load Chain. Default: load all chains --edgefile EDGEFILE Load fixed fragment file; one sequence of forced connections per line, separated by space. -e EDGE, --edge EDGE Forced edge: e.g. -e1,3 --fixed FIXED Same as --edgefile. --iterations ITERATIONS Iterations --json JSON If writing output pdb, also write JSON metadata. Default: 1. Options: 0, 1 --overwrite Overwrite files without prompting --verbose n, -v n verbose level [0-9], higher number means higher level of verboseness --ppid PPID Set the PID of the parent process, used for cross platform PPID }}} = Examples = = FAQ =