Structure Editor window To open the structure Editor window cick the Structure Editor or choose the Tools Structure Editor menu item e or open a structure by choosing the File I Open I Structure menu item and Structure Editor will start automatically. nly 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 I Structure Editor menu, and the Structure Editor is already opened, this window becomes active. To begin draw ing a chemical structure in Structure Editor, click one of the buttons on the vertical bar. Every time you dick one of these not represented in the menu. If the function of a button is not apparent from its appearance, simply point the urso at this button using the mouse and a hint will be displayed. we recommend trying out all the various features on a test structure
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 Stru cture 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
Default mode Generate Fragments Mechanisms Open Structure (Sub)Structure Search Save Structre Structure layout Print Structure Check structure Undo Clean Redo Mirror Cut Rotate ②日舀“XC田√》还 Single Bond Double bond Triple Bond Delete Past Benzene ring opy Six Membered Ring Templates Atom Properties Bond Properties Positive Charge Negative Charge Unspecified Charge Site:none Radical Select Unspecified Charge Site Tex 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 ba rs. A smaller window may prove advantageous if your program desktop is filled
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 Edito r window is more compact, but retains all the buttons on the button ba rs. A smaller window may prove advantageous if your program desktop is filled with other modules
sStructure Editor 自X√器还 H HO Unspecified Charge Site: TH+ C27H4SO'H+ 2387.362 In the Structure Editors 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 utton in the upper left comer in the structure Editor window Press the right mouse bottom v itch off the activated button and deselect all atoms Opening and Saving Structures To open or save a structure: Click on the Open Structure Save structure in the structure Editor window Choose the File I Open I Structure or the File I Save I Structure menu item If you are opening a file w hich contains more then one structure(*.sdf file), only the first structure in the file will be loaded into Structure 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
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 struc tures. 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 MOLfiles(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 Frontiers particularly useful features is the ability to restrict a search by a set of structural constraints, the so called GoodBad" ch comparing an unknown spectrum only with the spect ra 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 any thing that it is possible 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 graph ics to your individual report or pub lication needs. To open Structure Layout dialog window ●Cl button in the structure editor window Choose the Options I 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 in make the mechanism network unclear, especially for complex hydrogen rearrangement steps. a substructure search ignores the number and positions of hydrogen atoms. H HC、<CH H The structure layout settings apply to all structures in Mass Frontier simultaneously. This means that if you change a structure layout item all structu res in the structure Dior, Dhtabag ManageR, Fas feclunsms, Fragmentation Library, and Fmgments Comparator modules are affected
Structure Data Formats Structu re 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 spect ra 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 structu res 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: ructure Editor window 2. Click anyw here in the draw ing area to place the text. 3. Type the desired text. Confirm the text by clicking outside the text area or press any button in Structure Editor. ssible to creat notes. If you want to char do this in the Structure Layout dialog window in the Text tab. lote: Text notes are not associated with structures. As a result Open, Sav, Copy, and Paste actions apply to structure(s) only. When these ctions are applied the text notes are ignored even if a structure is selected together with a text. Additionally structure handling routines such as resuing, rotating, or mirroring can be performed only on structures
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 structu ral 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: 1. Click on the Text button in the Structure Editor window. 2. Click anywhere in the drawing area to place the text. 3. Type the desired text. 4. 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