For viewing and exploring proteins and small molecules. View atom positions, bonds, solvent-accessible-surfaces, and electron density. Perform and visualize molecular dynamics using built-in Amber parameters.

Conceptually similar to PyMol, Chimera, and Discovery Studio, with functionality similar to Coot and VMD as well.

Designed to be as easy to use, and fast as possible. Has tight integration with RSCB, Pubchem, drugbank, and Amber. Uses parallel computing to accelerate calculations. (GPU, SIMD, and thread pools.)

Download, unzip, and run.

Notes:

• On Linux distros that use Gnome (e.g. 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. See notes in the compiling section below about setting up Amber parameter files, and disabling CUDA.

• View the 3D structure of proteins and small molecules
• Visualize ligand docking
• Molecular dynamics, using Amber force fields, and the OPC water model
• WIP: This software is a platform for ab-initio simulations of electron density.

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.

Most UI items provide tooltip descriptions, when you hover the mouse over them.

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

• Proteins: mmCIF (.pdb supported removed; use mmCIF instead)
• Small molecules: SDF, Mol2, and PDBQT
• Electron density: 2fo-fc mmCIF, Map, and MTZ
• Force field parameters: dat, and frcmod (Amber)

If an nVidia GPU of at least RTX 3 series is available, molecular dynamics, docking, and electron density calculations will be performed using the GPU (via CUDA kernels). If not, the CPU will be used, leveraging thread pools and SIMD instructions. It uses all cores available, and either 512-bit, or 256-bit, SIMD instructions, depending on CPU capability.

Integrates the following Amber parameters:

• Small organic molecules, e.g. ligands: General Amber Force Fields: GAFF2
• Protein/AA: FF19SB
• Water: OPC

Currently, MD only supports polypeptides and small organic molecules. We plan to support carbohydrates, DNA, RNA, and lipids later. If you're interested in these, please add a Github Issue.

These general parameters do not need to be loaded externally; they provide the information needed to perform MD with any amino acid sequence, and provide a baseline for dynamics of small organic molecules. You may wish to load frcmod data over these that have overrides for specific small molecules.

This program can automatically load ligands with Amber parameters, for the Amber Geostd set. This includes many common small organic molecules with force field parameters, and partial charges included. It can infer these from the protein loaded, or be queried by identifier.

You can load these molecules with parameters directly from the GUI by typing the identifier. If you load an SDF molecule, the program may be able to automatically update it using Amber parameters and partial charges.

For details on how dynamics using this parameterized approach works, see the Amber Reference Manual. Section 3 and 15 are of particular interest, regarding force field parameters.

Moleucule-specific overrides to these general parameters can be loaded from .frcmod and .dat files. We delegate this to the bio files library.

We load partial charges for ligands from mol2, PDBQT etc files. Protein dynamics and water can be simulated using parameters built-in to the program (The Amber one above). Simulating ligands requires the loaded file (e.g. mol2) include partial charges. we recommend including ligand-specific override files as well, e.g. to load dihedral angles from .frcmod that aren't present in Gaff2.

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

The free camera mode 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

• Left backet: Previous view mode (sticks, surface mesh etc)

• Right bracket: Next view mode

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

Supports volumetric and isosurface views for electron density data, e.g. from Cryo-EM and X-Ray crystallography data. It can download this data from RCSB PDB, or load files directly. To open 2fo-fc and MTZ files, we use the Gemmi program. For convenience, we package it with the program's releases. For this to work, the gemmi folder we include must remain co-located with the program's executable. If not there, the program will attempt to run Gemmi from the system path. (E.g., installed as part of CCP4).

Can import Map files directly, and save load density to Map format.

Daedalus supports a very limited subset of PyMol's CLI interface. Supported commands:

• help: Lists commands
• pwd
• ls
• cd
• set seq_view

• fetch: Loads a protein from the RCSB PDB. e.g. fetch 1C8K
• save: Save the opened protein or small molecule to disk. e.g. save molecules/1htm.cif
• load: Load a protein or small molecule from disk. e.g. load ../1htm.cif

• show: Set the view mode. e.g. show sticks
• view: Save and load scenes. e.g. view v1, view v1 store, view v2 recall
• hide: Limited options available, e.g. resn HOH, hydro, chain, hetatm etc.
• remove: Limited options available, e.g. resn HOH, hydro, chain, hetatm etc.

• select resn: Select a residue by 3-letter amino acid identifier
• select resi: Select a residue by index
• select elem: Select an atom by element abbreviation

(sele works too)

• turn
• move
• orient
• reset

You may notice that this program places a daedalus_prefs.dae file in the same folder as the executable. This is a small binary file containing application state. It's what lets it remember the last file opened, current view settings etc. It will grow with the number of molecules you've opened, as it stores per-molecule settings. Deleting it is harmless, other than resetting these conveniences.

This application is pure rust, so compiles normally using cargo build --release, which produces a standalone executable. It requires these 6 Amber parameter files to be present under the project's resources folder at compile time. These are available in Amber tools. Download, unpack, then copy these files from dat/leap/parm and dat/leap/lib:

• amino19.lib
• aminoct12.lib
• aminont12.lib
• parm19.dat
• frcmod.ff19SB
• gaff2.dat

We provide a copy of these files for convenience; this is a much smaller download than the entire Amber package, and prevents needing to locate the specific files. Unpack, and place these under resources prior to compiling.

If you're not running on a machine with an nVidia GPU or without the CUDA toolkit installed, append the --no-default-features to the build command. This will disable GPU support.

If compiling with GPU support, you must set the environment var LD_LIBARARY_PATH (Linux) or Path (Windows) to your CUDA bin directory, e.g. C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v13.0\bin. You may also need the build tools containing cl.exe or similar in the path, e.g.: C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.44.35207\bin\Hostx64\x64

CUDA v13.0 or higher must be installed on the compiling machine, but is not required to run the program.

• Ribbon (cartoon) view is unavailable.
• Loading map (electron density) files that are very large (e.g. high detail, especially Map files directly available on RCSB, vice created from 2fo-fc) may crash the program.
• Opening electron density files in general can be slow. This can lead to the program starting slowly if it was last shut down with electron density data open.
• The GUI doesn't handle proteins with many chains well.
• Electron density isosurfaces are currently broken
• GPU on Linux is finicky at the moment. You might get an error on launch if not on an nvidia GPU with drivers installed, instead of falling back to the CPU. The latest linux drivers available on Ubuntu's official tool don't support CUDA 13, which is currently required. We provide CUDA and non-CUDA linux downloads until this is resolved.
• On some displays, dragging the MD time slider may also move the camera. To workaround, click the slider instead of dragging.