Structure Editor Window To open the Structure Editor window:
click the Structure Editor button on the main tool bar.
or choose the Tools | Structure Editor menu item.
or open a structure by choosing the File | Open | Structure menu item and Structure Editor will start automatically.
Only one Structure Editor window can be opened at any one time in the program. If you click the Structure Editor button, or you choose the Tools | Structure Editor menu, and the Structure Editor is already opened, this window becomes active.
To begin drawing a chemical structure in Structure Editor, click one of the buttons on the vertical bar. Every time you click one of these buttons the shape of the cursor will change to visually represent the engaged drawing mode. The vertical buttons, in contrast to the horizontal buttons, are not represented in the menu. If the function of a button is not apparent from its appearance, simply point the cursor at this button using the mouse and a hint will be displayed. We recommend trying out all the various features on a test structure.
Reduced Size of Structure Editor Window When you reduce the size of the Structure Editor window the button array on your desktop changes. The reduced Structure Editor window is more compact, but retains all the buttons on the button bars. A smaller window may prove advantageous if your program desktop is filled with other modules.
Restoring Defaults In the Structure Editor's default state all buttons are switched off and no atom or bond is selected. The plain arrow cursor indicates that the Structure Editor is in default state. To restore the default state of the editor, choose any of these methods:
Click the Default mode button in the upper left corner in the Structure Editor window.
Press the right mouse bottom.
Switch off the activated button and deselect all atoms.
Opening and Saving Structures To open or save a structure:
Click on the Open Structure or Save Structure button in the Structure Editor window.
Choose the File | Open | Structure or the File | Save | Structure menu item.
If you are opening a file which contains more then one structure (*.sdf file), only the first structure in the file will be loaded into Structure editor. Mass Frontier is a 32-bit application, so you can use long names to save structures. You can even save structures by their actual names (e.g. 1-Amino-2-hydroxyindane.mol).
Structure Data Formats Structure Editor supports two kinds of structure formats: MDL MOL-files (SDF-files), with the *.mol (*.sdf) extension, and HighChem MCS format (Maximal Compressed Structure), with the *.mcs extension. These formats are also supported in the Database Manager module. Templates are stored in MCS-format, using the extension *.tml. One of Mass Frontier's particularly useful features is the ability to restrict a search by a set of structural constraints, the so called "Good-Bad" list. For example, you can instruct the program to conduct a library search comparing an unknown spectrum only with the spectra of ketons. This feature provides an endless range of possibilities to target your search results with. The “Good-Bad” structures are stored in the directory ..\Constraints, and the structures are saved in MSC-format (*.mcs). The program automatically retrieves all MCS-structures from ..\Constraints directory and puts them in a “Good-Bad” list box in the Constraints dialog box.
Structure Layout Mass Frontier is a layout powerhouse. For structures, as well as for other objects, you can change almost anything that it is possible to change. Every layout setting change also affects printing and copying into Clipboard, except background color, which affects only screen display in the Mass Frontier program. The various layout items allow you to tailor the graphics to your individual report or publication needs. To open Structure Layout dialog window,
Click on the Structure Layout button in the Structure Editor window.
Choose the Options | Structure Layout menu item.
By default the symbols for hydrogen atoms attached to carbon atoms are not displayed (example a). If you wish to display them select Show Carbon Symbols (example b) in the Structure Layout dialog box. Hydrogen atoms are only displayed for carbons if the Show Carbon Symbols check box is clicked. Otherwise corresponding hydrogens are displayed for heteroatoms only.
Note:
If you draw nonisotopic explicit hydrogen atoms (example c) these are removed in the Fragments & Mechanisms window, as they can make the mechanism network unclear, especially for complex hydrogen rearrangement steps. A substructure search ignores the number and positions of hydrogen atoms.
The structure layout settings apply to all structures in Mass Frontier simultaneously. This means that if you change a structure layout item, all structures in the Structure Editor, Database Manager, Fragments & Mechanisms, Fragmentation Library, and Fragments Comparator modules are affected.
Note:
If you do not have a color printer and are printing in black and white, and you have set bright colors for bonds or atoms, the lines and fonts may appear indistinct. To avoid this problem, specify darker colors for all structural items, including spectra, chromatograms, and mechanisms.
Structure Text Note Structure Editor offers the possibility of labeling a structure or displaying a text note on the screen or on the printout.
To enter a text note:
Click on the Text button in the Structure Editor window.
Click anywhere in the drawing area to place the text.
Type the desired text.
Confirm the text by clicking outside the text area or press any button in Structure Editor..
It is possible to create up to 127 separate text notes. If you want to change the font, color, size, or background of the text notes you can do this in the Structure Layout dialog window in the Text tab.
Note:
Text notes are not associated with structures. As a result Open, Save, Copy, and Paste actions apply to structure(s) only. When these actions are applied the text notes are ignored even if a structure is selected together with a text. Additionally structure handling routines such as resizing, rotating, or mirroring can be performed only on structures.
Templates When you click the Templates button in the Structure Editor window, the Template dialog window appears. Mass Frontier comes with more then 200 predefined templates. To insert a template structure into Structure Editor:
Select a group of templates in the directory list box. You can do this using the arrow keys on the keyboard or clicking the appropriate name of the group.
Click any atom or bond, depending on whether you want to attach the template to an atom or a bond of a structure in Structure Editor.
The Template dialog window will then disappear and you can place or attach the chosen template.
Switch off the template button or restore the default state of the Editor.
Mass Frontier makes it easy for you to create your own group of templates or add a structure to an existing group. The templates are organized by directory. The template root directory is ..\Templates. Every group of templates is stored in a separate subdirectory of the template root directory. Subdirectories are named after compound groups (e.g. Steroids). The files within each subdirectory are named after actual structures using the extension *.tml (e.g. Cholesterol.tml). When you save a structure for template purposes select Template (*.tml) format in the Save as Type scroll box in the Save Structure dialog box. To build your own templates, follow these steps:
Draw a template structure.
Click on the Save Structure button in the Structure Editor window or choose the File | Save | Structure menu item.
Select Template (*.tml) format in the Files of type: combo box in the Save Structure dialog window.
Create or select a subdirectory in the directory ..\HighChem\Mass Frontier4.0\Templates for your new template.
Type name of your new template structure and click OK.
Selecting Atoms and Bonds Any modification that you make to a structure applies only to the selected atoms or bonds In addition, when a (Sub)Structure search is initiated, the program automatically uses the selected (sub)structure in Structure. Before you select one or more atoms you should restore the default state of the editor. To select a group of atoms that are next to each other:
Hold down the mouse button and drag a rectangle around the atoms you want to select.
The usual Windows convention for selecting multiple items applies. To select atoms at different locations, you should use the keyboard SHIFT key. You can select a group of atoms that are not adjacent in one of two ways:
Click the atoms you want to select, while holding down the SHIFT key.
Or hold down the mouse button and drag a rectangle around the atoms you want to select, while holding down the SHIFT key.
If you want to select all of the atoms and bonds in the structure:
Click the Select All button in the Structure Editor window or choose the Structure | Select All menu item.
Or double click anywhere in the draw area within Structure Editor, except on atoms and bonds.
Structure Editor offers two selection modes: Rectangle Selection and Lasso Selection. To choose the selection mode that fits your needs:
Click with the right mouse button on the Default Mode button and choose the appropriate selection mode from the popup menu.
Or click with the right mouse button anywhere in the draw area within Structure Editor, and click the Rectangle or Lasso Selection menu item on the pop-up menu that will appear in the draw area.
Atom Properties To change the charge state or isotope of an atom, or to change the element entirely, use the Atom Properties dialog box. To open the Atom Properties window, use one of the following methods:
Select the Atom Properties button in the Structure Editor window and then click the atom you want to change.
Or restore defaults, and then double-click on the atom you want to change.
In the Atom Properties dialog window, you can make the changes by clicking the appropriate element button, charge and radical check box, or nucleon number edit box.
Note:
All changes carried out in the Atom Properties dialog window will only affect a single atom.
If you wish to change an element that has a single character symbol, i.e. C, H, N, O, B, F, K, P, S, I, V, W, Y, U and R; a faster method is available:
Select all the atoms that you want to change and press the appropriate key on the keyboard. All the selected atoms will be transformed into the element you have chosen.
Chlorine (Cl) or bromine (Br) atoms can be set in a similar manner:
Select all the atoms that you want to change and press either the C (for chlorine) key or B (for bromine) key on the keyboard, while holding down the SHIFT key.
It is possible to use a substituent instead of a specific element. The symbol ”R” represents a substituent. A substituent can be with or without index. Substructure search and fragments generation algorithms consider substituents with identical indexes as equal and substituents with different indexes as not equal. When searching structures with substituents, please note the search rules that apply.
Bond Properties Bond Properties include bond multiplicity, bond style and bond color. To change the multiplicity of a bond,
Click the , or , or button in the Structure Editor window and then click the bond you want to change.
To change the color or optical orientation of a bond, use the Bond Properties dialog window. To open the Bond Properties window:
Click the Bond Properties button in Structure Editor and then click the bond you want to change. The Bond Properties dialog window will then appear.
Or restore defaults, and then double-click on the bond you want to change. The Bond Properties dialog window will then appear.
Mass Frontier automatically recognizes aromatic bonds in an appropriate six-membered ring or in polyaromatic structures. However, if unusual semiaromatic or aromatic resonance structures are required, the aromatic bond can be forced to selected bond(s) by checking the Force Aromaticity check box.
Copying Structure Mass Frontier supports extensive use of the Windows Clipboard for the exchange of structural information between modules. In addition, copy and paste functions may be used inside Structure editor. To draw larger structures efficiently, we recommended taking advantage of the copy and paste functions. To copy a structure or part of a structure into the Clipboard:
Select the structure or part of structure you want to copy.
Click the Copy button in the Structure Editor or choose Copy from the Edit menu.
Note:
Only the selected atoms and their associated bonds will be copied!
In addition to structure exchange between modules, Mass Frontier allows structure export to other programs that deal with structural information. When you copy a structure, Mass Frontier automatically copies two different formats into clipboard: structural information in MOL format and graphics in Windows Metafile Format (wmf). If you paste a structure into the structure editing software the MOL format will be used. If you paste the structure into any text editor, spreadsheet or any other program that works with graphics, the graphical information will be used. All these actions occur automatically so the user need not worry which format is used. Structure Exchange via Copy & Paste commands.
Pasting Structure If you have copied a structure or fragment anywhere in the program or in a third party structure drawing tool, you can paste it to Structure Editor. If necessary, the structure can be changed or corrected and then returned to where it originated. This is especially useful for structure elucidation. For example, you can copy a structure from the Database Manager window, paste it to Structure Editor, make appropriate changes, and then move it back to Database Manager. If the spectrum and the structural proposal are not consistent, the process can be repeated. To paste a structure to Structure Editor:
Click the Paste button in the Structure Editor.
Or choose the Paste item from the Edit menu.
If you have copied a structure or fragment in a program other than Mass Frontier, you can only paste this structure if the external structure drawing software supports MOL format and this format is activated. The majority of structure drawing tools support MOL format and usually have this format activated by default. If you paste a structure from an external source it may sometimes appear larger in Mass Frontier than in the original software. If this should happen, you can simply make the structure smaller using the Resize tool. Structure Exchange via Copy & Paste commands.
Moving Structure To move a structure in the Structure Editor:
Select the atoms or bonds you wish to move.
Point the mouse cursor at any selected atom or bond.
Hold down the mouse button and drag the selected structure to the new location.
Release the mouse button to drop the selected structure at the new location.
Resizing Structure To resize a structure in the Structure Editor:
Select the structure/or part of structure you wish to resize.
Click the Resize button , or select the Structure | Resize menu item.
Drag one of the small rectangles on the structure edge until the new size is achieved.
Release the mouse button.
Note:
If you drag one of the diagonal rectangles the aspect ratio will be kept constant during structure resizing.
Rotating Structure The Rotate Structure option allows you to twist a structure in any direction. The center of rotation, indicated by a small circle with a cross in the middle , can be moved to any location. To rotate a structure in the Structure Editor:
Select the structure/or part of structure you want to rotate.
Click the Rotate button , or select the Structure | Rotate item.
Move the center of rotation to the desired position by dragging the circle with a cross.
Drag any of the small rectangles on the structure edge to achieve the new angular position.
Cleaning Structure The Clean function allows you to achieve a professional look to your structures. In contrast to other commercial structure drawing programs, with Mass Frontier you can even clean up an individual part of a structure. For example, you can restrict cleaning to certain functional groups, while the main skeleton remains intact. However, the algorithm of cleaning 2D structures is a particularly difficult mathematical problem and has yet to be completely solved. As a result this function may, in some complicated cases, lead to structures you will not be completely satisfied with. If this should occur, simply use the Undo function. To clean a structure:
Select the structure/or part of structure you want to clean up.
Click the Clean button , or choose the Structure | Clean menu item
Note:
If you want to clean only part of a structure, the selected atoms must be connected, otherwise the message box appears to remind you that only cleaning of connected atoms is possible.
Checking Structures Structure Editor comes complete with a function for checking chemical structures. Structure Checker searches for formal errors and unusual structural features. If a structure is formally incorrect, or Structure Checker considers there is some doubt about its validity, a Structure Check Results window appears with a list of errors and warnings. When this window is closed the program automatically selects the atoms and bonds, which are considered incorrect. As mentioned in the Program Limitation section, structures that are not connected are considered to be mixtures, which are reported as errors.
To check a structure:
Click the Check Structure button in the Structure Editor, or choose the Structure | Check Structure menu item.
MS Calculations When you select a part of a structure, Structure Editor automatically displays the molecular formula and molecular mass of the selected atoms (F:) in the status bar of Structure Editor, together with corresponding loss (L:). You may find this information useful for simple consistency checking of mass spectrum and chemical structure.
