<code bash> 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

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