Daedalus: structural biology

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Goal: The easiest to use structural biology tool

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.

Blends functionality similar to PyMol, Chimera, Coot, VMD, GROMACS, and Avogadro.

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

Installation

Windows and Linux

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.

Mac, and linux distros we don't provide a binary for

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 either installing the CUDA toolkit, or disabling CUDA.

Functionality

• View the 3D structure of proteins and small molecules
• Molecular dynamics, using Amber force fields, and the OPC water model
• Visualize ligand docking
• Edit small molecules in 3D with integrated dynamics
• Visualize electron density from crystallography and Cryo-Em data
• Run ORCA quantum chemistry procedures on molecules (if ORCA is installed).

Molecule types supported for viewing and dynamics

• Proteins
• Small organic molecules (e.g. ligands)
• DNA and RNA; double and single stranded
• Lipids

Getting started

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.

Goals

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

File formats

• Proteins: mmCIF (aka PDBx)
• Small molecules: SDF, Mol2, GRO, XYZ, and PDBQT
• Electron density: 2fo-fc mmCIF, Map, and MTZ
• Force field parameters: dat, lib, frcmod, prmtop (Amber), and top (GROMACS)

A note on internet connectivity

This application can run smoothly without internet connectivity. If you do have internet, it has some API integrations which may help. For example, loading molecules automatically from PubChem, drugbank, and RCSB PDB. It can also download associated ligands for a protein, automatically download molecule-specific force-field parameters, and other party tricks.

Parallel computing

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.

GPU functionality requires Nvidia driver version 580 or higher.

Molecular dynamics

We use the Dynamics rust library for molecular dynamics. See that library's readme for details and assumptions.

Integrates the following Amber parameters:

• Small organic molecules, e.g. ligands: General Amber Force Fields: GAFF2
• Protein/AA: FF19SB
• Nucleic acids: Amber OL3 and RNA libraries
• Lipids: Lipid21
• Water: OPC

We plan to support carbohydrates in the future.

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.

For small organic molecules, we may compute force field types, partial charges, and dihedral overrides. These can be provided directly from FRCMOD files, or suitably annotated Mol2 or SDF files, but are often absent. The computations we use are similar in principle to Amber's Antechamber tool, and we use parameters from it.

For details on how 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, prmptom, and .dat files. We delegate this to the bio files library.

We load partial charges for ligands from mol2, sdf, xyz, and pdbqt 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.

Editing molecules

We provide an editor for small organic molecules. This is fully-3D, and has integrated dynamics, which can be run continuously while you edit. It ensures the molecules you create are realistic, and take the appropriate shape.

The camera

The camera is set up with 6 degrees of freedom, using either keyboard + mouse, or mouse only. This makes it easy to get any view of the system you want.

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

Free camera

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.

Arc camera

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.

Hotkeys

Most of this functionality is also available in the GUI, and you can find hotkeys from the GUI's tooltips. We recommend starting with the GUI, and integrating hotkeys into your workflow as you go, using tooltips. See below for a reference.

Mouse controls:

• 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. This also selects the molecule to manipulate.

Camera hotkeys

• 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)

Non-camera hotkeys

• Left arrow: select previous residue

• Right arrow: select next residue

• Left arrow: Select previous residue

• Right arrow: Select next residue

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

• Right bracket: Next view mode

• Semicolon: View/select level (Atoms, bonds, residues)

• Right bracket: Next view/select level

• M: Move a molecule with the mouse and scroll wheel

• R: Rotate a molecule with the mouse and scroll wheel

• Enter: Move the camera to the selected atom or residue.

• Esc: Clear selection, molecule manipulation modes etc.

• Ctrl + scroll: Change the fog distance. (hide distant atoms)

• Delete: Close the active molecule

Note: The molecule editor has a different set of hot keys; see its tooltips for details.

Reflections and electron density

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 this to work, the gemmi folder we include must remain co-located with the program's executable, or be on the system path. For convenience, we package it with the Windows release, and the linux install script optionally installs it with apt.

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

PyMol-like Command line interface

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

General

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

File IO

• 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

View and edit

• 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.

Selections

• 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)

Camera controls

• turn
• move
• orient
• reset

Selection modes

Using a dropdown in the UI, you can change selection mode between Atom, (covalent) Bond, and Residue. These are mostly self-explanatory. When selecting a component using right click, or toggling using the UI buttons or arrow keys, this changes what is selected, and the nature of information displayed. For example, in Bond mode, you can see bond length, elements of the atoms connected, and the expected oscillation frequency of the bond. In Atom mode, you can see dihedral angles, the atom name as part of its residue, the atom's force field name, and its partial charge.

Adding nucleic acids and lipids

You can add DNA, RNA, and lipids in various configurations without loading files; this program can create them procedurally using the GUI. It can create DNA and RNA from a given nucleic acid or amino acid sequence. It can create lipids arranged freely, as membrances, or as lipid nanoparticles (LNPs).

The preferences file

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.

Compiling

This application is written in rust, so it compiles normally using cargo build --release, which produces a standalone executable.

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.

Compiling with GPU support

If compiling with GPU support, your compiling PC must have the CUDA Toolkit, v13+ installed. 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.

Errata

• Only one protein can be loaded at a time
• 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.
• Minimizing may pause molecular dynamics computations.
• On some displays (Ones with pixel scaling), dragging the MD time slider may also move the camera. To workaround, click the slider instead of dragging.