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General Information

Here are general information about the Settings dialog window.

PySSA Settings

  • Overview

    In this dialog you can ...

    • change the workspace.
    • enable/disable the automatic startup of the Help Center window.
    • change the Cycles value for the distance analysis.
    • change the Cutoff value for the distance analysis.
    • change the background color.
    • change the ray-tracing renderer.
    • change the ray-trace-mode.
    • change the ray texture.

Details

Workspace

  • All projects are stored in this folder.
  • The default value is C:\Users\.pyssa\default_workspace.

Automatic startup of the Help Center window

  • Tick the checkbox, if the Help Center should open at application startup.
  • The checkbox is ticked by default.

Cycles value (Distance Analysis)

  • Defines the number of outlier rejection cycles for the structure alignment.
  • The default value is 0 cycles, that means all residues are used.

Cutoff value (Distance Analysis)

  • Every distance that is above the cutoff will be removed from the result if the number of cycles is greater 0.
  • The default value is 1.0 but is not used in the distance analysis because the number of cycles are set to 0.

Background color

  • Changes the background color of the current PyMOL session.
  • Black is the default value.
  • Two colors (black and white) can be used.

Ray-tracing renderer

  • Defines the renderer that is used during the ray-tracing process
  • The default renderer is PyMOL internal renderer.

Ray-trace-mode.

  • Defines how the colors look in the ray-traced image.
  • The default value is normal color + black outline
  • Experiment with different modes and see what fits best for your use case.

Ray texture.

  • Defines the texture PyMOL uses for the proteins during ray-tracing.
  • The default value is None.
  • Experiment with different textures and see what fits best for your use case.
See Also

Advanded Prediction Configuration

Settings