# Troubleshooting protein-ligand docking tutorial

**URL:** <https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011>\
**Category:** Uncategorized\
**Tags:** proteomics\
**Created:** [November 27, 2024, 10:26am UTC](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011 "2024-11-27T10:26:42Z")\
**Posts on this page:** 1\
**Showing post:** 2

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [November 27, 2024, 5:25pm UTC](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011/2 "2024-11-27T17:25:59Z")

</div>

Hi @FOZIAH_ALSHUBAILY

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](https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html)

And this was the advice about generating the graphics →

> [@protein-ligand docking visualization using NGLViewer](https://help.galaxyproject.org/t/protein-ligand-docking-visualization-using-nglviewer/6194/4):
>
> > we created that GIF by combining screenshots from two poses together  
> > if you got as far as creating the PDB files for the docked poses, you can click on the `Visualize this data button` on the datasets in your history  
> > then you have a choice of visualizations and you can pick NGLviewer

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](http://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](https://help.galaxyproject.org/docs?topic=11469)

Thanks! 🙂

---

_[View the full topic](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011)._