David-OConnor/daedalus: Protein and molecule viewer

For viewing and performing minor edits on moleculars; espsecially proteins and nucleic acids.

Conceptually similar to PyMol, Chimera, and Discovery Studio.
Designed to be as easy to use, and fast as possible.

Download, unzip, and run.

Notes:

• On some Linux distros (eg Ubuntu), run setup_linux_desktop.sh, included in the zip, to create a Desktop GUI entry.
• On Windows, the first time you run the program, you may get the message “Microsoft Defender prevented an unrecognized app from starting”. To bypass this, click More info, then Run Anyway.

Compile from source by downloading and installing Rust, then running cargo build --release from a CLI
in the project directory.

• View the 3D structure of proteins and small molecules
• Visualize ligand docking
• WIP: This software is a platform for molecular docking, and ab-initio simulations.

Launch the program. Either open a molecule using the “Open” or “Open Lig” buttons, drag the file into the program window,
enter a protein identifier in the Query databases field, or click I’m feeling lucky, to load a recently-uploaded protein
from the RCSB PDB.

• Fast
• Easy-to-use
• Practical workflow
• Updates responsive to user feedback

• Proteins: mmCIF and PDB
• Small molecules: SDF, Mol2, and PDBQT

There are two camera control schemes, selectable using buttons in the camera section of the GUI.

The free camera controls is intended to be used with a keyboard and mouse together. They operate on the perspective of
the viewer, vice the molecule. You can move and rotate and move the camera
in 6 degrees of freedom, allowing you to easily view the molecule from any perspective.

• Hold the left mouse button while dragging to rotate the camera in pitch and yaw.
• Hold the middle mouse button while dragging to move the camera left, right, up, and down.
• Scroll to move the camera forward and backwards.
• Scroll while holding left mouse button to roll.
• Right click to select the atom or residue under the cursor.

• W: Move forward

• A: Move right

• A: Move left

• D: Move back

• Space: Move up

• C: Move down

• Q: Roll counter-clockwise

• R: Roll clockwise

• Shift (left): Hold to increase camera movement and rotation speed.

• Scroll whlie holding left mouse: Roll (Alternative to Q/R)

• Left arrow: Select previous residue

• Right arrow: Select next residue

Similar to traditional molecular viewing software. The camera arcs (or orbits) around the molecule, when holding the left
mouse button and dragging. Other controls, like scroll wheel and middle mouse, operate similar to the free camera.
If orbit sel is set in the GUI, the orbit center will be the selected atom or residue, vice the molecule center.

• Esc: Clear selection
• Left arrow: select previous residue
• Right arrow: select next residue

• Cartoon view (Showing helices and sheets) is currently unavailable.
• The only van der Waals surface view currently available is dots, and it’s slow to build. Mesh WIP.
• The GUI doesn’t handle proteins with many chains well.
• Docking is inop.

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