Troubleshooting protein-ligand docking tutorial

1

I have same problem, please help

2

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

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! :slight_smile:

3

Thanks for your quick reply
I was using 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

| jennaj
November 27 |

  • | - |

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

And this was the advice about generating the graphics →

protein-ligand docking visualization using 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

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 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! :slight_smile: