Markush Viewer - View Markush Structures Organized

Markush Viewer
Markus Viewer Menu and Toolbar
Markus Viewer Panels
Examples

Markush Viewer Application

Markush Viewer is a desktop application of ChemAxon to view the various R-group definitions of Markush structures in an organized way. Markush Viewer represents the hierarchical nature of a Markush structure in graphical form. The structures of an opened Markush file will be identified, classified and organized as scaffolds and attached R-groups to help you follow each nested structure. Markush Viewer is part of the JChem Suite. Running this application, you need to have the JChem package installed on your computer.

Markush Viewer
layout

Figure 1. MarkushViewer layout

The application window contains the menu, toolbar, and three main panels of which one is closed by default.

Markush Viewer Menu and Toolbar

The menu contains "File", "View", and "Help" elements.

"File" menu options
- Open a molecule file (Ctrl+O), ;
- Exit Program (Alt+F4).
You can toggle the following elements in the "View" menu:
- "Fragments and Markush": Sets the display options of the structures on the Fragments and Markush panels. You can make visible the followings:
  - "Atom properties": Default setting is on;
  - "Lone pairs": Default setting is off;
  - "Valence errors": Default setting is on;
  - "R/S labels": Default setting is off;
  - "E/Z labels": Default setting is off;
  - "Implicit hydrogens": Sets the visibility of implicit hydrogens:
- "Toggle Fragments autosize" : According to the size of the different R-group fragments, the cells will be autosized in the View panel. Default setting is on;
  Please note: You can resize the height of the rows by using Mouse-drag on the lower edge of the molecule panel.
- "Always display scaffold in Fragments" : Displays the relevant scaffold of the selected R-group. Default setting is on;
- "Toggle nesting view" : Opens bottom panel. The step-by-step route to the selected R-group will be displayed. Default setting is off;
- "Toggle molecule display in tree" : Expands the boxes of the tree to show the structure of the molecule. Default setting is off;
- "Toggle separator lines visibility" : Turns on /off the vertical separator lines between generations. Default setting is off;
- "Toggle node lines visibility" : Turns on/off the lines connecting the parent molecules and their children. Default setting is on;
- "Collapse all nodes" : Closes all nodes. Default setting is off;
- "Expand all calculated nodes" : Expands all the nodes of the tree you expanded before to show molecule structures. Default setting is off.
"Help" menu
- "Help" (F1);
- "About".

Markush Viewer Panels

The left "Tree" panel houses the tree-like composition of the Markush structure;
The right "View" panel shows the corresponding structure(s) selected in the left panel;
Optional "Nesting" panel at the bottom of the window. The embedding of the selected R-group can be followed in this field. Open this field with button .

Note: Dividers between the fields are flexible; grab and drag them to resize fields.

Tree Panel Options

The Markush structures of the opened file are organized and arranged in the Tree panel. The scaffold is presented on the first (parent) level of the tree, and the associated R-groups are classified as its children. The scaffold(s) and attached groups are denoted by named boxes. Unless the Markush structure has molecule title, the parent level boxes are named as: "Markush(n)", Scaffold. Child level boxes are marked with the relevant R-group definition (e.g.: R1, R2,...Rn), followed by the number of members of each R-group in parentheses.

If the opened Markush structure is a colored searching result, then the respective tree nodes are colored as well. See Figure 4.

To view any scaffold or R-group definition, select the relevant node. The structure(s) of the chosen element will be presented in the View panel. The selected items are highlighted in the Tree panel.

Figure 2. Select a node and see the relevant structure(s) in the View panel

You can select more than one structure from the tree using Shift+Left-Click or Ctrl+Left-Click to display them in the View panel at the same time.
Note: Shift/Ctrl+Arrow keys work for selection as well.

Figure 3. Select more nodes and see structures in the View panel

Figure 4. Markush structure as a colored searching result

View Panel Options

View panel displays structures that are selected in the Tree panel. The panel has two alternative tabs: "Fragments" and "Markush".

"Fragments" tab displays the members of the selected element in a grid view array. See Figure 2 and Figure 3.
- The sign of every fragment can be found above it.
- The scaffold is always visible - even if no tree node is selected - if "Always display scaffold in fragments" is on.
- You can resize the height of the rows by using Mouse-drag on the lower edge of the molecule panel.
- You can move the structure within its cell by using Ctrl+Mouse-drag.
- You can zoom in the structure within its cell by using Ctrl+Mouse wheel.
  
  Note: Double click in the cell restores the original size and position of the structure.
"Markush" tab shows the full Markush structure centralized on the selected node(s).
- You can zoom in the structure by using Ctrl+Mouse wheel.
- You can move the structure by using Ctrl+Mouse-drag.
  
  Note: Double click in the field restores the full size of the Markush structure.

Figure 5. Change between "Fragments" and "Markush" tabs in View panel

Nesting Panel Options

Nesting panel displays the step-by-step route of embedding of any selected R-group starting from the scaffold.

Select a node (group R27) in the Tree panel and follow its evolution in the Nesting panel. When more nodes are selected, they change to be highlighted by pink color, the uppermost of them by red color. This red node is displayed in the Nesting panel, and the previous and next buttons are activated to turn to the previous or next node within the selected ones.

Figure 6. Follow the embedding of the selected R-group in Nesting panel

Examples

Open a molecule file.
- The file loads into the Tree panel.
Switch on the Nesting panel.
Select more nodes from the tree (Ctrl/Shift+Left-clilck).
- The selected nodes are highlighted in the Tree panel.
- In the Fragments tab of the View panel, you can see the structures of the selected fragments. Note that the "Always display scaffold in Fragments" is on by default. Your selections are arranged below the appropriate scaffold.
- In the Nesting panel, you can follow the route to the selected R-group. In case you select multiple nodes from the tree, the previous and next buttons are active.
Study the Toolbar elements.
- Toggle off "Always display scaffold in Fragments".
  - Unless you select the relevant scaffold in Tree panel, its structure will not be visible in View panel. Note: If you select a scaffold in Tree panel, its structure will retain in View panel after toggle off "Always display scaffold in Fragments" button.
- Toggle off "Toggle Fragments autosize" button.
  - All the selected fragments are in fixed, uniform height cells in the View panel.
- Expand the nodes of the Tree panel to show the small structures of each node.