GitHub - dtegunov/cube: Particle picking for tomograms (original) (raw)

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• README

Cube – making sub-tomogram picking suck slightly less.

You will need

• Precompiled binaries (compiling the code yourself will likely fail because I don't synchronize updates for all dependencies)
• Windows PC with a GPU that supports OpenGL 4.4, the latest drivers and .NET Framework 4.7 installed.
• Tomographic volume in MRC format.
• Optionally, particle coordinates either as a tab-delimited text file (XYZ columns), or a STAR file using Relion's column names (i. e. rlnCoordinateX etc.).

Controls

• Pan the view by clicking the mouse wheel and dragging.
• Zoom in and out by holding Shift and scrolling.
• Go through slices by scrolling.
• Click the left mouse button and drag to synchronize all three planes to the mouse position. During this operation, scrolling through slices still works, so you can easily explore all 3 dimensions without pressing anything extra.
• Release the left mouse button to create a new particle. If you don't want to create one, hold Shift while releasing the button.
• Delete the currently selected particle by pressing Delete.
• Delete any particle by right-clicking it.
• Cycle through particles by pressing the Left and Right Arrow keys.
• Adjust particle positions by clicking on them and dragging. While dragging, scroll the mouse wheel to adjust the third coordinate on the fly.
• Alternatively, you can go to a specific position or move a particle by adjusting the numeric sliders at the top left corner of each view. Either click the slider, enter a value and confirm with Enter; scroll the mouse wheel while hovering over one; or click the slider and drag the mouse vertically.

Authorship

Cube is being developed by Dimitry Tegunov (tegunov@gmail.com), currently in Patrick Cramer's lab at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany.