Foldit Standalone Quickstart Guide

1. Visit https://els2.comotion.uw.edu/product/foldit-standalone.
2. Select "Order Now" under "Foldit Standalone Academic License" on the right.
3. Click "Checkout Now" and follow prompts to obtain a license for Foldit.
4. You will receive an email with instructions to access the download page.
5. Select the "Foldit Standalone" download link for your platform.

If you use Foldit Standalone in your work, please cite:

Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B. Siegel, Firas Khatib and Seth Cooper. Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinformatics 2017 btx283.

To load in files, choose the "Import PDB/FASTA" button when the program starts. Then select (at least) a ".pdb" or ".fasta" file. The program determines file types by their extension. Depending on the other files you select, different session features will be enabled. For example, selecting a ".density" file will enable electron density.

Here are a few example setups. For each example, you will need to select all files with the same base filename for import.

• example_pdb - basic PDB
• example_fasta - basic FASTA
• example_guide - includes a guide structure
• example_density - includes electron density; enables the electron density panel
• example_template - includes a template; enables the alignment panel
• example_ligand - includes a ligand as a custom residue type
• example_dna - includes DNA
• example_rna - includes RNA

Here are some example Rosetta Script files: repack_no_design.xml, repack_design.xml (these may take up to a minute or two to complete).

• Please download the latest version from the licencing site above.
• Reference sheet with useful key commands and other tips.
• If you are on macOS, please make sure to move the FolditStandalone.app to your /Applications folder before running.
• If you are on macOS and get a message about the application being from an unknown developer when you try to launch it, try right-clicking on the application and selecting "Open".
• If you are encountering trouble, you may find more information in the log file. It can be found at:
  • Windows: C:/FolditStandalone/log.txt
  • macOS: FolditStandalone.app/Contents/Resources/log.txt
  • Linux: [working directory]/log.txt
• If you are having issues importing files during an existing session, try restarting the program and importing them from the starting screen.
• If you are having issues importing a large number of different file types, try a setup with fewer file types.
• UserEcho site for feedback.