1. Open a terminal:
- on Linux: Ctrl+Alt+T usually works, otherwise browse your application menus
- on Windows: double click adf_command_line.bat in your ADF installation directory (e.g. C:/ADF2016.106), enter 'sh' to go to a shell
 
2. cd into the directory where your trajectories are located with the terminal
3. Running ChemTraYzer:
 
  assuming your trajectory is called traj.rxkf
 
  a) run the processing step (with default values)
     $ADFBIN/startpython $ADFHOME/scripting/chemtrayzer/processing_scm.py traj.rxkf
 
  b) run the analysis step (with default values)
     $ADFBIN/startpython $ADFHOME/scripting/chemtrayzer/analyzing_scm.py traj.rxkf
 
   you will probably want to adjust the settings. The available options are shown by calling the scripts without arguments, e.g.
    $ADFBIN/startpython $ADFHOME/scripting/chemtrayzer/analyzing_scm.py
 
4. Results
 
  there are several output files, the most relevant ones being:
 
  reac.spec.tab
  -------------
  1st line: indices of the species, e.g. S1;S2;S3;etc...
  2nd line: SMILES of the species, e.g. ;C;CC;CCO;CCOO;CO;O;[H];etc...
  3rd - end: timestep, counts of the species, e.g. 150;0;0;2;... // step 150, current count of S3 == 3
 
  reac.rate.tab
  -------------
  1st line: indices of the reactions, e.g. t [steps];R0;R0*;R1;R1*; // a "*" marks the back reaction
  2nd line: the reactions formulated with the species indices, e.g. ;S0 + S0 + S0 + S13 -> S65;   // see reac.spec.tab
  3rd line: the reactions formulated with sum formulas, e.g. CH3 + H -> CH4, etc...
  4th -...: timestep;rate constant of the reaction; rate constant of the back reaction; etc...
 
  reac.pic/
  ---------
  folder containing the 2D structures (if obabel was able to create them)
  reac.pic/xyz/ xyz files of the species as they first appeared in the trajectory