User Guide

EasyHybrid is a graphical environment for pDynamo3, designed to make it easy to visualize, edit, inspect, and simulate molecular systems. It runs on both Windows and Linux. This user guide was created on Linux Mint, but the interface should be very similar on any system. If EasyHybrid is properly installed, you can launch it by running the following command in the EasyHybrid main directory.

~/something/EasyHybrid3$ python3 EasyHybrid.py 

The main window of EasyHybrid can be divided into five sections, as shown in Figure 1. In the following sections, we will provide a more detailed explanation of how each tool works and what it can do.

A brief description for the parts mentioned in Figure 1: 

1 - main menu: Contain all the functions available in EasyHybrid. 

2 - main toolbar: Contains the main features of EasyHybrid and can be divided into file tools, selection toolbar, pDynamo toolbar and selection type box (Figure 2). 

3 – GL Area: This is the interactive space for visualizing three-dimensional objects. All active objects are displayed here. The basic mouse (Figure 3) and keyboard commands for interacting with 3D models are as follows:

Button 1: Selects objects in the GL area (applicable to both view and edit mode).

Button 2: Invokes the GL area menus.

Button 3: Centers the viewable object on the selected atom.

Button 1 + Mouse Movement: Rotates the 3D models.

Button 2 + Mouse Movement: Zooms in or out of the field of view.

Button 1 + Mouse Movement + Shift: Enables area selection when the 'viewing' option of the selection box is active.

Button 1 + Mouse Movement + Ctrl: Rotates the camera on the Z axis (depth).

4 - System Treeview: The system treeview (Figure 4) displays all systems currently loaded in memory along with their respective viewable objects. Since it is possible to work with multiple systems simultaneously, the active system—the one used in simulation routines—is indicated by a radio button in the first column of the treeview.

Each loaded system has a collapsible header (treeview item) for easy navigation. The interface uses reference colors for each system, and by default, new viewable objects assign the system’s reference color to the carbon atoms. You can customize these colors in your preferences.

The treeview includes two columns labeled “V” and “F” for viewable objects. The “V” column indicates which objects are currently visible in the GL area, while the “F” column displays the number of frames available for each object.

Mouse Button 3 opens the treeview context menu, which provides options to change system settings and access additional functionalities.

5 - Status bar: The properties of the active system in memory (identified by the selected radio button in the first column of the system treeview) are displayed in the status bar. When the active system is changed, the status bar updates accordingly. The displayed properties include the total number of atoms, frozen (fixed) atoms, atoms in the QC region, force field, QC method, non-bonded model, and more.

6 -status notebook / sequence viewer: It shows the history of the main routines executed within the interface. The colors are used to associate the record with the receptive systems (color of references). This widget also includes a tab called the Sequence Viewer, which displays the amino acid sequences (using the one-letter code) of the objects currently active in the main treeview. The Sequence Viewer is interactive, allowing the user to select portions of the system directly through it.