View source for 2022 DOCK tutorial 1 with PDBID 6ME2

= Introduction = 

===DOCK===
(some info about DOCK)

===6ME2===
(some info about the structure)

===Required Software===
(chimera, dock,...)

= Seawulf: Getting Started = 
===Basics of the Command Line/Terminal===

===Logging and navigating Seawulf===

===File transfers to/from Seawulf===

= Chimera: Getting Started =

===Searching for/Downloading files from the PDB===
(explain the protein data bank, how to find files, reading through the attached literature, downloading in different formats, etc)

===Opening and viewing PDB files===
(show some screenshots and explain file types)

===First-steps for visualizations in Chimera===
(show how to change view settings (i.e., black vs. white background), how to select parts of the structure based on a number of criteria, color parts, delete parts, etc) 

===Saving sessions===
(explain how to save all the configurations of a session)

===Saving files: file formats===
(explain mol2, pdb, etc, maybe some words about properly organizing folder structures and properly naming files in the process)

= Dock Prep =

===Initial investigation/preparation===
(put in here anything you notice when first opening up a sometimes messy structure--in 6ME2's case we had to remove detergents and water that were far from the of-interest binding site, handle non-standard amino acids, etc. Compare to the structure described in the literature to see if everything is accurate)

===Isolating the ligand and receptor===
(show how to create two separate files, one with just the ligand and one with just the receptor)

===Adding Hydrogens===
(show how to add hydrogens in the isolated structure files)

===Adding Charges===
(show how to add charges in the structures)