# Troubleshooting protein-ligand docking tutorial **URL:** \ **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:** 3\ **Page:** 1
**Author:** ![FOZIAH\_ALSHUBAILY](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/foziah_alshubaily/32/5172_2.png) [@FOZIAH\_ALSHUBAILY](https://help.galaxyproject.org/u/FOZIAH_ALSHUBAILY)\ **Post date:** [November 27, 2024, 10:26am UTC](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011/1 "2024-11-27T10:26:42Z")
I have same problem, please help ---
**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")
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! 🙂 ---
**Author:** ![FOZIAH\_ALSHUBAILY](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/foziah_alshubaily/32/5172_2.png) [@FOZIAH\_ALSHUBAILY](https://help.galaxyproject.org/u/FOZIAH_ALSHUBAILY)\ **Post date:** [November 28, 2024, 6:12am UTC](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011/3 "2024-11-28T06:12:24Z")
Thanks for your quick reply I was using [galaxy.org](http://galaxy.org) as the tutorial advice to use it but the galaxy version sometimes can’t be changed in some tools as per the tutorial i got everything right, but visualizing is the problem visualization could be done from Galaxy platform, or external tools should be used Thanks again Prof. Fawzia A. Alshubaily Biochemistry Department Faculty of Science King Abdulaziz University > ![](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/45/27_2.png "jennaj") | [jennaj](https://help.galaxyproject.org/u/jennaj) > November 27 | > > - | - | Hi [@FOZIAH\_ALSHUBAILY](https://help.galaxyproject.org/u/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 → > ![](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/simonbray/48/1258_2.png)[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 > > 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! ![:slight_smile:](https://emoji.discourse-cdn.com/twitter/slight_smile.png?v=12 ":slight\_smile:")