Basic Features of Marvin JS

Importing and Saving Structures

Importing a Structure

Marvin JS handles MDL Molfiles V2000 (.mol extension) and ChemAxon Marvin Documents (.mrv extension) as input files. However, other file types (MDL RXNfile and RGfile, SMILES, ChemAxon Extended SMILES, SMARTS, ChemAxon Extended SMARTS, InChi, Name, CML, MDL Molfile V3000, MDL RXNfile V3000, MDL RGfileV3000, MDL SDfile, ChemAxon Compressed Molfile, ChemAxon Compressed SDfile, and XYZ) can also be imported if the appropriate webservice is available.

Press the Import button on the General toolbar to open the Import pop-up window. The dialog can be opened by pressing the "Ctrl+O" keyboard shortcut, too. Open the structure file in *.mol or *.mrv format with a text editor (e.g., Windows's Notepad), select all, and copy the file contents to the clipboard then paste it into the input area of the Import window. At the top of the window you can select the appropriate file format from a drop-down list. Finally, pressing the "Import" button loads the structure on the canvas.

Saving a Structure

A structure can be saved either in ChemAxon Marvin Document format or in MDL Molfile V2000 format. In order to export in other file formats (MDL RXNfile and RGfile, SMILES, ChemAxon Extended SMILES, SMARTS, ChemAxon Extended SMARTS, InChi, InChiKey, Name, CML, MDL Molfile V3000, MDL RXNfile V3000, MDL RGfile V3000, MDL SDfile, ChemAxon Compressed Molfile, ChemAxon Compressed SDfile, XYZ, CDX, and SKC) the appropriate webservice has to be available.
Please note that if you have a single step reaction on the canvas, then only those file formats will be available for saving which support reaction files.

To save the structures on the canvas, click on the Export button on the General toolbar, which opens the Save dialog window. Alternatively, you can use the "Ctrl+S" keyboard shortcut as well. In this window you can see the canvas contents in the default ChemAxon Marvin Document format. The structure file format can be changed by selecting an option from the drop-down list of supported file formats. To save that to a file, push the Download button at the bottom of the dialog window, click on the created link, and save the file with the preferred name and route. Alternatively, you can paste the structure source into a text editor and save it from there. In case of CDX and SKC file formats, only the first option can be carried out.

Saving as Image

In order to save an image of the structure in Marvin JS, select "Image" in the Save dialog. The supported image formats are PNG and JPEG. You can also set display options detailed elsewhere, determine the color of the image background (transparent or white), and set the width and height of the image.

Select and Delete

Selection

Clicking on the lower right corner of the Selection button of the Tools toolbar you can choose between two options:

Rectangle Selection:
Freehand Selection:

Using either selection mode, an atom or a bond can be selected by clicking on it. Please note that in this case the bond gets selected along with the connected atoms. If you want to select a bond without its atoms, you have to choose Freehand Selection, and select the middle of the bond. Alternatively, press the "Ctrl" button and click on the bond, while either selection tool is active.

With Rectangle Selection, you can select an area in rectangle mode while with Freehand Selection the area swept by the red line will be selected.

The background of atoms and bonds will become green when they are selected. In either selection mode, hovering over an atom or a bond, its background becomes green. When you click on this background, the green highlight gets lighter indicating that this part got selected.

Whole molecules can be selected by double-clicking on them. The result is the same as it would be using Rectangle Selection. Whole structures, fragments of molecules, or even several molecules can be selected at the same time.

• Separate parts of a molecule or even different molecules can be selected at the same time if the Shift button is pressed during selection.
• The "Ctrl+A" keyboard shortcut can also be used to select the whole content of the canvas.
• To clear the selection, you can press the "Esc" button, or simply click on a blank area on the canvas. If there is not any selection on the canvas, pressing the "Esc" button activates the Rectangle Selection tool.

Delete

Once you have made a selection (atom, bond, fragment, or a whole molecule), you can delete it either by clicking on the Delete button on the Tools toolbar or pressing the "Del" button on the keyboard.

Selecting the Delete tool and clicking on an atom or a bond erases said atom or bond. In case of deleting a bond, its atoms will not disappear from the canvas. On the other hand, if you erase an atom, its bonds are also deleted.

The Delete button also works as a rectangle selection tool: click on the button and select the parts you want to erase (the selected parts are highlighted in red). When you release the left mouse button, the highlighted parts will be erased.

You can clear the whole canvas with one click using the Clear button on the General toolbar or pressing the "Ctrl+Del" keyboard shortcut.

Cut, Copy, and Paste Options

To copy a molecule or a fragment you have to select it first. The Cut and Copy buttons on the General toolbar or in the contextual menu place the content of the selected area on the clipboard. The content of the clipboard can be imported to the canvas with the Paste button on the General toolbar. Their conventional shortcuts, "Ctrl+X", "Ctrl+C", and "Ctrl+V" can be used as well.

Another option for copying is to drag the selected structures while you hold down the "Ctrl" key. A copy of the selected structure is placed on the canvas when you release the left button. Note that the original object remains selected, so it can be multiplied several times.

Direct copy-paste between Marvin JS and other applications is available in MRV and MDL Molfile (V2000 only) formats. If the extended functionalities provided by JChem Webservices are also available, then structures can be pasted on the Marvin JS canvas in any of the supported text-based file formats (such as SMILES, Name, InChi...). Please note that copying content to the clipboard from Marvin JS is possible only via the Ctrl+C keyboard shortcut. This action always copies the structure in MDL Molfile (V2000) format. Similarly, if you want to paste chemical structures from the clipboard onto the Marvin JS canvas, you have to use the Ctrl+V shortcut.

If you use Marvin JS with a Firefox browser, please note, that copy-paste between Marvin JS and another applications works only with Firefox 22.0 and with newer versions.

Drawing Chemical Structures

Drawing atoms

You can choose from several options to draw a new atom or to modify an already existing one:

• An atom can be inserted by using one of the most frequently used atom buttons on the Atoms toolbar. The chosen atom appears on the tip of the cursor and you can place it on the canvas with a left-click.
• Any of the known elements can be selected from the Periodic Table, the button of which you can find on the Atoms toolbar. Choosing an element, its atomic symbol will appear on the tip of the cursor and you can place it on the canvas several times. At the same time, the Periodic Table window closes automatically.
• Atoms can be placed on the canvas using the keyboard. By typing an atomic symbol, it will appear on the tip of the cursor, and can be placed on the canvas with a left-click or pressing "Enter". Although they are not listed in the Periodic Table, deuterium and tritium symbols (D and T, respectively) can also be used this way.
• When a non-metallic atom is placed on the canvas, it will be automatically completed with implicit hydrogens according to the free valences of the atom. Display of implicit hydrogens depends on the current option in the View Settings dialog box. Metallic elements are exceptions to this rule, they are added to canvas in zero oxidation state.
• Atoms on the canvas can be replaced using either of the above mentioned methods. If you select several atoms at the same time, you can change them simultaneously using either the keyboard or the Periodic Table.
• Instead of standard atomic symbols, you can use any label for atoms by defining an atom alias in the Atom Properties dialog.
• Query atoms can be part of molecules (query structures) as well. To use these atoms, select their combo button on the Atoms toolbar. Pseudo atoms, which stand for an "Any" type query atom, can also be created through this button: click on the "question mark" in the query atom list and define the label you want to use with your pseudo atom in the dialog then close the dialog with the "OK" button and click on the atom you want to change into a pseudo atom. Note that pseudo atoms can be defined in the Atom properties dialog, too. A special class of pseudo atoms are the Homology Groups, which are also available from the Atom properties dialog.

Drawing bonds

• To create a chemical bond between two atoms on the canvas select the appropriate bond type using the Bonds combo button on the Tools toolbar, click on one of the two atoms, and drag the bond to the other atom.
• Selecting a bond type and clicking or dragging the cursor on the canvas will create a new bond with the default length and with carbon atoms on both ends.
• When a bond tool is active and the cursor is over an atom, a grey colored image of a bond in the selected type will appear, ended by a carbon atom. Pressing the "Shift" key will change the bond direction. Click on the atom will place the bond in this position. You can also draw a new bond by dragging from an already existing atom. Just like in the previous case, the length of the bond is the default value, and a carbon atom is on its other end.
• Bond type can be changed by selecting the new bond type from the toolbar and clicking on the bond on the canvas. The bond type can be selected by typing the appropriate shortcut, too. If the cursor is over the canvas, typing a shortcut will select the appropriate bond mode (the Bonds button is activated). However, if the cursor is over an existing bond, typing a shortcut will modify the type of the given bond only. In this case the selected mode (the active button) will not change.
• Note that repeated clicking on a bond will change its type depending on the currently active bond type. If the selected bond type is Single, successive clicks on a bond will change its type from single to double and vice versa. If Double bond type is selected, successive clicks on a bond will alternate its type between Double and Triple. Clicking on a directed bond (Single Up, Single Down, Single Up or Down, or Coordinate bond) will change the bond direction.
• Drawing molecules can be made much faster by using the Drawing tool of the Bonds combo button. With this feature, you can create the framework of complex structures without releasing the mouse button. When you draw a bond, grey dots appear indicating potential directions for the next bond. In the default case, these dots are the vertices of a hexagon, while they will be rearranged into a pentagon if you press down the "Shift" key. Dragging the cursor towards one of these dots, you can add a new bond to your molecule. While drawing a molecule, you can change the type of the last atom by typing a new atomic symbol. Clicking on a bond when the Drawing tool is active will change the bond type according to the Single-Double-Triple sequence.
  
• When more than one bonds are selected in a structure, selecting a new bond type will change every selected bond.

Drawing a molecule

Molecules can be created by connecting atoms with different chemical bonds or with the use of templates from the Templates toolbar.

You can create alkyl or conjugated hydrocarbon chains of arbitrary length using the Chain button on the Tools toolbar. A chain can be created as a new molecule or it can start from an already existing atom on the canvas. After selecting the button you can draw the alkyl chain by dragging or clicking repeatedly on the starting atom. The length of the chain is shown on the tip of the cursor. During drawing, the new chain can be rotated around its starting atom to the desired orientation by dragging. You can create a conjugated polyene chain by pressing the "Ctrl" button when chain-drawing.

Marvin JS supports different substructure group (S-group) types:

• Generic S-groups can be used in chemical structures, e.g., for visualizing solvent molecules or other compounds in a complex structure.
• Predefined abbreviated groups can also assist you to create complex molecular structures. For selecting an abbreviated group, use the Abbreviated Groups button of the Tools toolbar. When a group abbreviation has been selected from the list of the appearing dialog box, you can decide whether to place it on the canvas in contracted or in expanded form. For the latter option set the Expand checkbox in the dialog. Closing the dialog with the "OK" button will place the group on the tip of the cursor, from where you can put it on the canvas with a left-click (connect it to an already existing structure or start a new molecule). Learn more about abbreviated groups and their handling.

Merging structures

In Marvin JS you cal also merge separate fragments. Merging is helpful if you want to create ring systems (spiro, fused, or bridged ring systems: one, two, or more than two atoms in common, respectively) or to connect chain-like substructures. For merging two structures, one of them should be selected. When you hover the cursor over the selected fragment, the cursor will change to "move" type (crossed arrows) indicating that the fragment can be moved. Dragging the selected fragment until one or more of its atoms overlap with the "host" molecule atoms will merge the two structures.

Templates can also be merged with a molecule on the canvas. Choose a template from the toolbar (it appears on the tip of the cursor) and move it close to the atoms of the existing structure. When the distance between them has become sufficiently small, the possible merging points will be indicated by blue circles. Left-click will put the template in the merged position.

Spiro ring system	Fused ring system

Sprout drawing

Single atoms can be connected to non-terminal atoms in a "sprouted" position. Select an atom symbol, hover the cursor over the atom to which you want to attach the new atom, and press the "Shift" key to see the result of sprouting. Click on the non-terminal atom to attach the new atom to it.

Symmetric templates (cyclohexane, cyclopentane, benzene, pyrrole) can be connected to an atom with a single bond: select the template from the Templates toolbar and hover the cursor over the desired atom to see a grey colored image of the template showing its would-be position. Clicking on the atom will connect the template to the atom with a single bond: one of the implicit hydrogens of the atom will be replaced by the template. Please note that non-symmetric templates (including naphthalene) cannot be sprouted.

When sprouting, the template and the connecting single bond can be rotated around the connecting atom of the original structure by dragging.

If you want to avoid sprouting, hold down the "Shift" key while clicking on the selected atom. In this case the attaching atom of the template will not replace the connecting atom of the original structure.

A template can be attached to an already existing bond which is about the same length as the template's bond: clicking on the bond connects the template to the selected bond. The template is rotated automatically in order to fit the chosen bond perfectly.

• Pressing the "Shift" button and holding the left mouse key while sprout drawing mirrors the template to the other side of the bond. The side of the bond to place a template can also be altered by dragging the template to the appropriate side.
• When the pyrrole template is selected, and you hover over a bond, pressing the "Space key will rotate the pyrrole, so you can alter the orientation of the template easily.
  

Transformations

Dragging structures

After selecting them, whole molecules or fragments (parts of molecules) can be moved on the canvas. When you hover the cursor over the selected structure, the "move" cursor will appear indicating that the highlighted part can be dragged on the canvas. If you select a whole molecule, it will be translated without any modifications, but when the selection contains only a fragment, the molecule will be distorted due to the changes in bond lengths and bond angles. Note that the positions of the atoms within the selected fragment are fixed, so only the bonds between the selected and non-selected part of the molecule will be distorted.

Rotating in 2D

When a structure has been selected, it can be rotated around its center in two dimensions.

The pink circle with a dot is the center of the selected area (pivot point). The molecule can be rotated around this point by clicking on the green dot and dragging the cursor on the canvas. During dragging, you can see the angle of rotation near this green dot. By default, rotation is done in 6° increments. For continuous rotation hold the "Shift" key while rotating.

When a whole molecule is selected, the original center of rotation can be relocated by dragging. In this case, if the new rotation center is too close to its original position, it will be snapped back to it. However, pressing the "Shift" key while dragging the center of rotation allows it to be as close to its original place as you wish. Moving the center lets you rotate the molecule around any point of the canvas. The image of the starting structure remains displayed in grey during rotation.

When a selected part is only a fragment which connects to the rest of the molecule with one bond only, you cannot move the pivot point (which is gray in this case). In such cases the rotation center will be that atom of the selected fragment which connects to the non-selected part of the structure.

Rotating in 3D

Structures on the canvas can be rotated in three dimensions. Please note that during 3D rotation, every molecule you have on the canvas will be rotated and their coordinates will change accordingly. If you want to rotate the molecules in 3D, push the 3D rotate button on the Tools toolbar, then drag the cursor over the canvas. While rotating, you can see the current angle of rotation around the vertical (y-) and horizontal (x-) axis next to the cursor, as well as on the two axis at the edges of the canvas.

If you hold down the "Shift" key while rotating, you can rotate the structure around the vertical or horizontal axis only, depending on the main direction of dragging (i.e., if you move the cursor from left to right, the structure will be rotated around the y-axis, while if you drag the cursor up and down, the molecules will be rotated around the x-axis).

Mirroring structures

Molecules or fragments can be mirrored either horizontally or vertically using the Mirror Horizontally or Mirror Vertically options in the pop-up menu. For mirroring, you should select the molecule or fragment concerned, right-click inside the selected area, and select the appropriate menu option. Mirroring is possible only for whole, unattached molecules or for fragments which connect with no more than one bond to the unselected part of the structure. In any other case, the mirror options remain inactive.

Finally, it has to be mentioned that the rules of undoing/redoing are the same for every kind of transformation: an event begins with pressing down the mouse button and ends with releasing it. The whole action between these two points can be undone or set back in one step.

Atom Properties

Currently Marvin JS supports the display of atomic charges, isotopes, monovalent radicals, enhanced stereo specifications, and manual atom maps as atom properties. All of these attributes can be set in the Atom properties dialog window available from the pop-up menu after a right-click on the atom.

The dialog provides options for changing atom type, setting new atomic symbols, or defining properties of atoms. You can choose from the following atom types: Element, Query, R-group, List/NOT list, Pseudo, or Homology Group. Choosing any of these types, only the relevant property fields appear on the dialog. For example, in case of a pseudo atom, there are three properties available: pseudo, charge, and enhanced stereo. Previously defined properties can be removed by clicking on the Remove property button.

These properties can be set for several atoms at the same time, by selecting the atoms in question and then opening the Atom Properties dialog from the context menu. In this case, only those properties are editable which are permitted for every selected atom type, and the same changes will be applied to every selected atom. If one or more of the selected atoms has/have attached properties, you can delete them by using the respective Remove property buttons.

If you use an 'Alias' for an atom, the label given in the textbox will replace the standard atomic symbol on the canvas, but the atom type remains unchanged. With the exception of enhanced stereo notations, atom properties are not displayed when an atom alias is used; however, they preserve their previously defined values and can be modified later.

The enhanced stereo notations (Off, Absolute, And, Or) can be added to chiral atoms (marked with wedge bonds) individually in order to assign them to stereogenic groups. The default value is the "Off" identifier, while in case of "Or" and "And" groups a number should accompany the identifier. If you leave the number field empty, number 1 will be associated with the group identifier automatically. Learn more about enhanced stereo specifications in Marvin JS.

The "OK" button closes the window, and the changes appear in the structure. As a result, a charge will appear as an upper right index of the given atom, while the mass number (isotope type) will be displayed as an upper left index. In case of hydrogen isotopes (deuterium and tritium), their specific atomic symbols can be used (D and T, respectively), or they can be displayed as ²H or ³H, too.

Note that atomic charges can be modified using the Increase Charge/Decrease Charge buttons on the Tools toolbar, too.

Drawing Graphical Objects

Currently, you can draw rectangle boxes in Marvin JS by using the Box button on the Tools toolbar. The boxes can be moved or resized and the color of their edges can be changed via contextual menu.

Display Options

Structure display options

Structure display options can be modified with the View settings button on the General toolbar, which opens the View settings dialog box. The options offered here are the following:

• Show chiral flag: The visibility of the "Absolute" chiral flag can be turned on/off.
• Show valence errors: Marking of atoms with incorrect valence can be turned on/off.
• Show lone pairs: The visibility of lone pairs of atoms can be turned on/off.
• Index atoms: When checked, the atom indices (the order of the atoms put on the canvas) are displayed.
• Use CPK colors: When checked, the atoms are displayed colored according to the Corey-Pauling-Koltun convention. The two halves of a bond between two atoms will receive the color of the atom they are connected to.
• Show carbon labels: When checked, the carbon atom labels become visible.
• Implicit H: To display the automatically added necessary hydrogens on atoms, an option from the drop-down list in the View Settings window should be chosen. These options are the following:
  
  

  Off	Disable implicit hydrogen display on every atom.
  Hetero	Display implicit hydrogen display on hetero atoms.
  Hetero and Terminal	Display implicit hydrogens on hetero atoms and terminal carbons. (Default setting)
  All	Display implicit hydrogens on every atom.

• Display: You can choose between two display options: wireframe or ball and stick. On the image below, you can see an example for each display mode both in 2D and 3D mode:

	Wireframe	Ball and Stick
2D
3D