selections
EasyHybrid's selection function works with a paradigm very similar to PyMOL, dividing selections into two basic types: Viewing Selections and Picking Selections. You can switch between one type or another by changing the status of the checkbox on the toolbar of the main window (Figure 1).
Figure 1: EasyHybrid provides a selection box where you can switch between two modes: Viewing Selections and Picking Selections.
Viewing Selections
In the Viewing Selections mode, users can select groups of atoms for various purposes. These include freezing coordinates, changing colors, assigning atoms to the quantum region, pruning or deleting parts of the system, and more. The selections work by addition, meaning that when a group of atoms is selected, any subsequent atoms selected will be added to the already selected set of atoms. Users can interactively select atoms by clicking on the desired atom in the GL main window area. The following selection options are currently available:
By Atom: Selects only the clicked atom.
By Residue: Selects the entire residue to which the clicked atom belongs.
By Chain: Selects the entire chain to which the clicked atom belongs.
By C-Alpha Selects only the clicked C-Alpha atom.
By Molecule: Selects the entire molecule to which the clicked atom belongs.
By Solvent: Selects only the atoms corresponding to solvent molecules.
These selection types provide flexibility in choosing specific sets of atoms for various operations within EasyHybrid. Figure 2 illustrates an example of the atom or group of atoms selected by clicking on the beta carbon of an aspartic acid residue centered on the screen.
No selecion
By Atom
By Residue
By Molecule
Figure 2: EasyHybrid some Viewing Selection types.
Additionally, this mode allows selections to be made by area using one of the options mentioned above. To do this, the user can combine the Shift key + Mouse Button 1 and move the cursor to establish the desired selection area. Figure 3 shows a set of atoms selected by area using the simpler '1. By Atom' criteria.
Shift key + Mouse Button 1 and move the cursor to establish the desired selection area
Atoms selected by area. Atoms selected by area are limited to only those that are visible on the screen. In this mode, you can only select atoms that are currently visible within the viewing area.
Figure 3: Selection by area.
EasyHybrid selections also employ click-on and off-click criteria. This means that to exclude a group of already selected atoms, the user can click on them using one of the predefined selection criteria. By clicking on the selected atoms, they can be deselected or excluded from the current selection.
Picking Selection
This alternative selection mode operates on a different paradigm. In this mode, only four (4) atoms can be selected. However, the order in which they are selected is preserved and utilized for situations where it is advantageous, such as calculating distances, angles, dihedrals, reaction coordinates, and so on. The selected atoms are visually represented in the GL area by tags labeled as #1, #2, #3, and #4 (Figure 4).
Figure 4: Picking Selection. Atoms were selected sequentially.
If an atom is mistakenly selected in this alternative mode, it can be replaced by deselecting it through the click-on and click-off process. By clicking on the incorrectly selected atom, it will be deselected, and then a new atom can be added to the selected group by clicking on the desired atom. This allows for easy correction and adjustment of the selected atoms in the group. Figure 5 shows the relocation of selection #2 from the beta carbon to nitrogen.
Figure 5: Relocation of selection #2 by click-on and click-off process.