e2pathwalker.py

e2pathwalker.py is a component of Pathwalker, described in the following publication:

• 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

• 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] <pdb file>

        Find paths between two atoms in a PDB model. You can also specify two PDB files to calculate an RMSD.

        Use "--solve=<solver>" 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