Let’s start over in a new thread since the other one is older.
For reference, this is the tutorial → Hands-on: Protein-ligand docking / Protein-ligand docking / Computational chemistry
And this was the advice about generating the graphics →
So, my question back is, where are you having trouble? Have you tried to run the tutorial workflow on the data to see if that produces the correct answer? If yes, you can use it to compare to, since that can usually isolate the step where something went wrong.
Please give that a try. The UseGalaxy.eu server might be best for this, but we can investigate at any of the UseGalaxy servers. Try running the tutorial, then we can help to look into why things are failing. You could even share both histories: your manual steps and the workflow run. How to share your work for questions and feedback is in the banner at this forum, also here → How to get faster help with your question
Thanks!