Quick Start Guide: Exercise 1


Loading and Preparing a Protein Structure

Set up a new project and import a structure, then clean up the structure with the Protein Preparation Wizard. This structure will be used in many of the following tasks.

Starting a new Maestro project

Maestro displays an empty, temporary (“Scratch”) project when you first launch Maestro. You can start adding structures immediately, but we suggest setting a working directory first, so that Maestro knows where to find and save files. Then name and save the project, so that all subsequent changes are saved automatically.

  • Choose File > Change Working Directory... from the top menu
  • In the Change Directory dialog, navigate to your chosen working directory, then click Choose; the dialog closes
  • Click the File menu again and choose Save Project As...
  • In the Save Project dialog, type “FXa.prj” and click Save; the dialog closes and the new name appears on the title bar of the Maestro window

Importing and preparing a protein

Follow the instructions below to download a structure from the internet. To read in the file from a local directory, use File > Import Structures... instead.

  • Choose File > Get PDB... from the top menu
  • In the Get PDB File dialog, type “1FJS” into the first field and click Download; the structure will appear in the Workspace, with a confirmation banner
  • Click the Prepare link on the banner to open the Protein Preparation Wizard (PPW)
  • Click the Preprocess button on the Protein Preparation Wizard
  • After a minute or two, you may get a warning about “Overlapping Atoms”; just click OK
  • Optionally click Optimize on the third tab of the PPW (“Refine”) to fix the overlapping atoms; otherwise, just close the panel

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