Graphical function

1. Foreword

• The selectable units (Atom, Residue, Chain, etc.) appearing in the graphical interface are collectively referred to as Object hereinafter.

• Object is classified as:

  • Protein, whose lower level is: Chain → Residue → Atom.

  • Ligand.

  • Solvant, including Water and Other Solvant.

  • Metal、Ions.

  • Pocket, both are cuboids.

  • Surface.

• A single Object, or a collection thereof, is called an Entry, and appears once as the smallest unit in the Entry List.

2. File

Import Structure

• General Toolbar Menu → File → Import Structure.

• Select the file Select Files:

  • Protein: .pdb.

  • Ligands: .sdf and .mol.

  • Check is supported.

• Show in the 3D Works pace: You can choose whether to show in the 3D Works pace.

  • If it is not checked, it will also be displayed in the Entry List at the file level.

• Replace Works pace: You can choose whether to replace the Objects in the current 3D Works pace.

  • If checked, the Objects of the original Entry List will not disappear, but will all become Hide status (hidden, not displayed, not appearing in Structure Hierarchy and 3D Workspace).

Get PDB

• General Toolbar Menu → File → Get PDB.

• Enter the corresponding PDB ID.

3. Entry List

• A window that presents an Entry in a hierarchical manner.

  • Objects that users are most concerned about in this project are displayed here.

  • The operations for the Object to enter the Entry List include: Import Structure/Get PDB, import through various Functions, and manually add the objects that need the most attention in 3D Workspace.

• Objects that are in Show in the Entry List are displayed in the Structure Hierarchy and 3D Workspace windows.

• Object operations are supported in the Entry List:

Name	Operation	Before	After	Tips
Multi-select	Press Ctrl/Command , click Object or hold down Shift, click the start point , hold down Shift, and click the end point
Drag	Select the corresponding Object with the mouse, press and hold the mouse, drag to the target position, and release
Rename	Double click Object
Split Into Ligands, Water and Other	Hover the mouse to the right button of the corresponding Object , select the Split Into Ligands, and Water and Other.
Duplicate	Hover over object Right click and select Duplicate
Delete	Hover over the corresponding Object Right click and select Delete
Group	Check to the corresponding Object Right click and select Group
Ungroup	Hover over the corresponding Group Right click and select Ungroup

4. Structure Hierarchy

• All Objects in 3D Workspace are displayed in a file-level manner, and expansion to the Atom level is automatically supported

• Measure (Distance, Angle, Dihedral), Label, Surface added in 3D Works pace can also be selected and operated in Hierarchy

• Object in Structure Hierarchy supports check, but does not support dragging

• Object operations are supported in the Structure Hierarchy:

Name	Operation	Before	After	Tips
Copy to New Entry	Mouse over to the right button of the corresponding Object and select Copy to New Entry
Extract to New Entry	Mouse over to the right button of the corresponding Object and select Extract to New Entry
Delete	Hover over the corresponding Object Right click and select Delete
Invert	Hover over the corresponding Object Right click and select Invert

5. 3D Workspace

• Objects in show state in Entry, presented in 3D Workspace in the form of 3D graphics, are the most important working window of Hermite platform.

• Full Objects and Structure Hierarchy are linked one by one.

• 3D Works pace Top Toolbar:

Name of the operation	Icon	Display	Remarks
Pick Level
Select Proteins
Select Ligands
Select Solvents
Expand			Select Ligand then Expand to select the surrounding 10 Å Objects
Measure
Interaction			Intermolecular interaction
			Intramolecular interaction
Label
Surface			Example showed the upper left corner of the picture, generating Surface for ligands.
Ribbon
Line
Stick
Ball & Stick
CPK
Setting			Protein coloring, set according to Residue, Chain, Hydrophobicity, Sencondary Structure and Antibody Structure; Ligand coloring, set according to Element and Atom Charge; Surface shading, set according to Residue, Chain, Hydrophobicity, Atom Charge, Solvent Accesibility; Transparent: set the transparency of the Surface.

• 3D Works pace Sidebar:

Name of the operation	Icon	Before	After	Remarks
Zoom In
Zoom Out
Reset
Focus
Save as .png		——	——	Save the picture
Refresh		——	——	Refresh
Label				Temporarily close, click again to open.
Measure				Temporarily close, click again to open.
Interaction				Temporarily close, click again to open.
Ribbon				Temporarily close, click again to open.
Surface				Temporarily close, click again to open.

6. Sequence Viewer

• And select the amino acid in the window, the same will be displayed in 3D.