quickstart# Terminal, Shell, & Bash Wtf is a Terminal? Example: Opening the Terminal App $SHELL Example: Bash Shell Commands Navigating Starting Location! Where Are We? What Files/Folders are Here? How to Make a New Folder/Directory? Enter/Exit Folders What are Paths? File Management Copy using cp Copy Folders with cp -r Moving & Renaming with mv Move/Rename Files and Folders Deleting Files and/or Folders with rm Deleting Multiple Files Deleting Folders Text Editors vi/vim How to Use vi/vim? Save & Quit Supercomputers What is ssh? What is Slurm? Accessing the HPC Remote Login What is the hostname? Task: Accessing the HPC HPC Job Managmer SLURM Language HPC Resources Pre-Installed Softwares Slurm Scripts Directives (#SBATCH) Python & Conda Conda Molecular Structure Files What are PDB files? What are XYZ Files? Exploring PDB Files Viewing the Contents of 1AKI.pdb What are ATOM lines in PDB files? ATOM Lines (PDB 1AKI) Chain Identifiers (Column 5 of ATOM)? Example with SpyCas9 Ternary Complex Chains are Separated by TER Lines What is Occupancy? What is B-factor? Summary Records in PDB Files What are XYZ Files? Example with Alanine Dipeptide Open the ala.xyz File Additional Resources Briefly, Molecular Dynamics Classical Mechanics
