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Windows installation instructions

The Pathways plugin was originally designed for POSIX-compliant platforms. Installing it on Windows is possible, but if you have access to a Linux or MacOS machine, I strongly recommend using it. If not, here are installation instructions for Windows.

Since a number of users have recently had issues with installing the plugin under Windows, here are step-by-step installation instructions:

  • Download a zip archive (pathways-master.zip) of the plugin code from https://github.com/balabin/pathways
  • Unzip the archive anywhere, e.g., in your home folder. That will create a folder named pathways-master
  • Make a permanent folder for the Pathways plugin, e.g., C:\Users\nopphon\pathways (hereafter Pathways home folder)
  • Copy Tcl scripts pathways-master/pathways/pathways.tcl, pathways-master/pathways/pkgIndex.tcl, and pathways-master/pathways/collective.tcl to the Pathways home folder
  • Copy the pathcore utility binary for Windows (pathways-master/pathways/pathcore/bin/pathcore_windows.zip) to the Pathways home folder and unzip the file. That should extract a file called pathcore.exe
  • Install VMD, following the directions from http://www.ks.uiuc.edu/research/vmd
  • Add to the VMD startup file vmd.rc (probably C:\Users\nopphon\vmd.rc ; if not, search for the file) the following lines
    global env
    lappend auto_path $env(HOME)/pathways
    These lines tell VMD to look for the Pathways plugin in that directory
  • Add the Pathways home folder to your environmental variable PATH (e.g., following https://www.c-sharpcorner.com/article/add-a-directory-to-path-environment-variable-in-windows-10 or any other manual on the topic)
  • Reboot, start VMD, open Tkconsole, and try running the following command there:
    pathcore
    If you see a pathcore greeting, you are all set and can start using the Pathways plugin right away. Otherwise, try some troubleshooting, starting with this:
    Does VMD see the plugin? Open Tkconsole and run the following command there:
    package require pathways
    Does Windows see the pathcore executable? Open a terminal and run the following command there:
    pathcore
  • Delete the pathways-master folder - you no longer need it.