Daedalus molecule viewer

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.

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

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

Functionality

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

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.

Goals

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

File formats

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

Molecular dynamics

Integrates the following Amber parameters:

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

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.

(todo: info on loading mol-specific frcmod data automatically)

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.

This program can automatically load ligands with Amber parameters, for the set called Amber Geostd. 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.

The camera

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.

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.

Camera Hotkeys (Also available as GUI buttons)

• 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

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.

Non-camera hotkeys

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

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. Currently, to convert 2fo-fc files to map data, you must have Gemmi available on your PC's Path. We include the Windows version of Gemmi with the release packages.

Can import Map files directly. MTZ support is not yet available.

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

Compiling

This application is pure rust, so compiles normally using cargo build, which produces a standalone executable. It requires these 5 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

Erratta

• Molecular dynamics dihedral-angle parameters are temporarily disabled.
• Ribbon view is currently unavailable.
• Opening a molecule by drag + drop may not work until minimizing/unminimizing the program
• Loading map 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.
• The GUI doesn't handle proteins with many chains well.