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Groel Demo Program Flow

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shadow_walker edited this page Aug 6, 2015 · 2 revisions

This was listed under https://github.com/GorgonCryoEM/Gorgon/issues/39 which is a general testing workflow. But, the flow listed is specific to the groel demo. So, it is moved here for reference.

Program Flow: http://gorgon.wustl.edu/pages/userGuide.php

  1. Load Volume: “densityMap.mrc”, “wireframe” option.
  2. Load Skeleton: “densityMap-skeleton.mrc”
  3. Load Helix Annotations: “helices-densityMap.wrl”.
  4. Load Sheet Annotation: For our GroEL example, no sheets were identified using SSEHunter and SSEBuilder.
  5. Load C-Alpha Atoms: For the demo, no C-alpha atoms will be loaded.
  6. Load Sequence and SSE Prediction: “groel-segment.seq”. To open the file from the menu bar, select “File>Open>Sequence and SSE Prediction…”.
  7. Generating a helix correspondence: “Actions>Secondary Structure Elements> Find Alpha-Helix Correspondences”.
  8. Helix Lengths: “helix-lengths.sse”.
  9. Sequence: The sequence file is identical to the file Sequence and SSE Prediction file that was loaded in section 2.6. If the file is not pre-populated, select the file again using the file select button to the right of this option.
  10. Finding a correspondence: The list of results can be used as reference. Need to save the results.

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