Structure Building

The structure building panel is designed to handle multiple structures at the same time. Initially the structure panel is empty. The user can start building a structure from a common core motif selected from the "File -> New" menu. To add subsequent structures using one of the core motifs the user can chose from the "Structure -> Add structure" menu.

Only tree-like glycan structures can be built. The residues are always added to the last selected residue. If no residue is selected a new structure is created and the residue is added to it. The substituents are treated as residues. A new residue is added by chosing from the "Structure -> Add residue" menu. Common terminals motifs can be added by chosing from the "Structure -> Add terminal" menu. A residue can be inserted before the current selection by clicking on "Structure -> insert residue before".

The properties of a residue (such as anomeric state, chirality and anomeric atom) and the position of the linkage to its predecessor can be set using the dialog activated by "Structure -> Residue properties". The type of the reducing end of the selected structure can be changed by clicking on "Structure -> change reducing end type". In this way labels and markers can be added to the structure. The mass of the marker is added to the total mass of the structure.

Fuzzy structures with uncertain antennae positions can be created by adding a bracket to a selected structure with the "Structure -> Add bracket" command. The antennae can then be added to the structure by selecting the bracket and adding the desired residues.

Export to file

The content of the structure panel can be saved to file, using the internal string format, for later retrieval. Otherwise, the structure drawings can be exported into file in several graphical formats (PS,EPS,PDF,SVG,JPG,BMP,PNG,GIF) using the menu "File -> Export to graphical formats".

Selection and Navigation

A single residue is selected by clicking the mouse left button on it. If the <ctrl> button is pressed, the residues that are already selected will remain in the same state, otherwise they will be deselected. If the <shift> button is pressed all the residues on the path connecting the last selection and the current one will be selected as well. By pressing the mouse left button outside of any residues and dragging it, the rectangle selection tool will be activated. When the mouse button is released all the residues in the rectangle area will be selected. If the <ctrl> button is pressed, the residues that are already selected will remain in the same state, otherwise they will be deselected. To select all residues of all structures just press >ctrl+A< or go to "Edit -> Select all". The currently selected structure is the one containing the last selected residue.

By clicking <ctrl> plus one of the arrow buttons the selection is moved from the last selected residue to the nearest residue in the direction indicated by the arrow. If no residue is selected, the selection is placed on the reducing end of the first or the last structure (depending on the arrow button).

Cut and Copy

All the usual cut/copy/paste operations are implemented in the GlycoWorkbench. The selected residues can be cut/copy from a location and then pasted in a different location in the same window. If no residues are selected when performing the "paste" action a new structure will be created, otherwise the content of the clipboard will be added to the last selected residue. The selection can also be pasted in a different window of the GlycoWorkbench. Finally, the copied residues can be pasted as an image in a graphic editor or Word document.

Drag and Drop

By pressing the mouse left button on a single residue or a group of selected residues, the drag and drop mode is activated. The selected residues can be dragged to any part of the drawing canvas. When the mouse button is released the dragged residues will be moved to the final location. If the button is released upon an existing residue, the selection will be added to it, otherwise a new structure will be created containing the selected residues. If the <ctrl> button is pressed the selection will be copied from the original location to its destination, otherwise the selected residues will be deleted from the original location. The selection cannot be dragged outside the current drawing canvas.

Visualization Options

The orientation of the drawn structure can be changed from right-to-left to left-to-right, to bottom-to-top to top-to-bottom, by clicking on "Structure -> change orientation". The orientation will affect also the way fragments are drawn in the fragment panel. The cartoon notation used to represent structures can be changed from the menu "View". Currently, three notations are supported: CFG standard, CFG black and white, Oxford. The visualization of linkages information is controlled with the "View -> show linkage info" command. In the same menu with the command "View -> show masses when exporting" it is possible to activate/deactivate the display of mass information in the exported/printed structure drawings.