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Reproduce guide

This guide is to reproduce Fig. 4 of our paper.

Video guide

  1. Install, and enable CUDA
  2. Demo Usage Scenario 3: Identify unknown densities

Text guide

  1. Download DiffFit-0.6.2-py3-none-any.whl
  2. Follow the installation guide
  3. Download the repository and unzip it to your working directory (which is your Desktop if you are on Windows or your home folder if you are on Linux).
  4. Open ChimeraX, launch DiffFit, go to the Settings tab, change Fit atoms: to All atoms.
  5. Go to the Disk tab, set the parameters as below:
    1. Target Volume: DiffFit-main\dev_data\input\domain_fit_demo_3domains\density2.mrc
    2. Structures Folder: DiffFit-main\dev_data\input\domain_fit_demo_3domains\subunits_cif
    3. Structures Sim-map Folder: DiffFit-main\dev_data\input\domain_fit_demo_3domains\subunits_mrc
    4. Target Surface Threshold: 1.44
  6. Click Run!
  7. With a RTX 4090 GPU, it takes about 14 seconds to finish the computation. If there is no CUDA-enabled GPU, the computation might take a few minutes to finish.
  8. When the computation finishes, DiffFit's View tab will open. The whole view should be very similar to Fig. 4 now. To get an even closer image, do the following:
    1. In the DiffFit View tab's table section, click the first row and then the second row.
    2. At the right of ChimeraX, there is a panel named Models. One row should give you I7M317_D1.pdb. Stay with this row.
    3. At the right of ChimeraX, there is a panel named Volume Viewer. Under it, there is a gray square next to an eye, click the gray square, set Alpha channel to 125.
    4. Drag and dock the DiffFit window to the left of ChimeraX.
    5. Hold the left mouse button in the viewport in the middle and drag to rotate so that the view is the same as in the Fig. 4.
    6. Change the background to white by clicking White, the 6-th last button in the top panel of ChimeraX.
    7. The numbers in the table will be slightly different. Because there are some random generators in the computation. (By default, DiffFit randomly seeds 1000 initial placements for each structure and optimizes them to better placements.)

Following a similar process and with the help of the detailed documentation, one should also be able to roughly reproduce Fig. 1, 5, 6, 7, and Table 1, 2, 3.