Provide instructions on how to do that in colab (user must click on Files icon on left hand side of UI)
Add a screenshot of what a visualisation of traj.pdb in VMD should look like. Mention PBC visualisation artefacts.
e.g.
Exercise 4. Download "bss_traj.pdb" and compare it to "traj.pdb" from method 1. What are the differences?
Is the intention to visualise both trajectories to comment on the size of the water boxes and the placement of the protein ? It's unclear how users should inspect the files (a text editor would be misleading).
In section_1/protein_ligand_complex.ipynb
Exercise 2. Download the "traj.pdb" file and visualize it.Provide instructions on how to do that in colab (user must click on Files icon on left hand side of UI)
Add a screenshot of what a visualisation of traj.pdb in VMD should look like. Mention PBC visualisation artefacts. e.g.
Exercise 4. Download "bss_traj.pdb" and compare it to "traj.pdb" from method 1. What are the differences?Is the intention to visualise both trajectories to comment on the size of the water boxes and the placement of the protein ? It's unclear how users should inspect the files (a text editor would be misleading).