How To Use Basic MarvinSketch Functions

Table Of Contents

Create New Molecule

A new, blank molecule is created when you first launch MarvinSketch. You can immediately begin working with this molecule. A MarvinSketch window can hold only one molecule at a time, so all work you do within the canvas is considered part of the same molecule. You can create a new, blank molecule at any time during your session by choosing File > New > Clear Desk from the menu bar. This will clear the desk and discard any unsaved changes to the molecule you were previously working with (but you can get it back using the Undo option).

The application allows you to work with multiple molecules in multiple windows by choosing File > New > New Window .

Open an Existing Molecule File

You can open existing molecule files (from supported file formats) by choosing File > Open on the menu bar. It will load the content of the molecule file into Marvin and discard any unsaved changes.

You can also Paste existing structures from other windows to the open molecule, as well as Drag&Drop a molecule file into the Marvin window. Both actions will add the new structure to the currently open molecule without overwriting the content of the canvas.

Save Molecule

Save Molecule File

You can save the molecule to any of the supported file formats. This will allow you to open and work with this molecule later. The default behavior of the Save button is to save the molecule to the same file it was opened from, in the same format. If you want to change the file name or format, choose Save As. If you are working with a new molecule, Save will function the same as Save As.

Save As Image

The Save As Image choice in the File menu allows you to save an image of the molecule in the sketcher. Marvin supports the following image formats: JPEG, PNG, PPM, POVRay, and SVG. Please note that the saved image cannot be edited in Marvin.

Print

You can print an image of the current molecule by choosing File > Print. If you print from a single page document, if the size of your molecule(s) is bigger then the paper size, it will be shrinked to one page.

How to Work with Multipage Molecular Document

How to create a multipage molecular document

• The items in the View > Pages menu are enabled
• A navigation statusbar appears on the bottom of the window
• The frame of the pages appear on the canvas, while the title, the margins and the page numbers are displayed on each page

How to navigate in multipage molecular documents

The navigation statusbar and the items in the View > Pages menu are available only if the Multipage document checkbox is set. The statusbar contains information about the current page number in a textfield and the number of all pages on a label. It also contains a collection of buttons to aid your quick navigation in the document. You can go the the first, previous, next, and last page using them. Alternatively, you can go directly to a specific page by entering a number in the current page field and pressing enter.

All the navigation possibilities: go to first, previous, next, last, specific pages are available from the View > Pages menu as well. In addition, some automatic page zooming functions are also available in this menu, such as:

• View > Pages > Fit page height adjusts the height of the current page to the height of the canvas.
• View > Pages > Fit page width adjusts the width of the current page to the width of the canvas.
• View > Pages > Fit page adjusts the height and/or the width of the current page to see the whole page, and places it centralized within the canvas.

How to Draw Structures

You can create structures using atoms, bonds, and templates.

Atoms

1. Select an atom from the Atoms Toolbar, the Periodic Table dialog, or by shortcut.

2. Move the mouse into the molecule canvas. You will see the symbol of the selected item at the tip of your cursor. It can be placed in the molecule by left-clicking on the desired location.

   • Marvin is chemically intelligent. It will account for implicit hydrogens and set the charge according to valence rules.

3. You can replace any atom in the molecule by placing a new atom on top of it.

Bonds

1. Select a bond type using the Bond toolbar button or by shortcut.

2. To link two existing atoms, click on one then drag the cursor to the other.

   • Marvin will allow you to draw a bond between any two atoms in the molecule. Valence errors will be highlighted (if that option is enabled).

3. To draw a bond from a single atom, simply click the atom. A carbon atom will be added at the other end of the bond.

4. If you add a bond to empty canvas space, a carbon atom will be added to each end of the bond.

5. You can replace any bond in the molecule by placing a new bond type on top of it.

6. Bond types can also be changed using the Bond pop-up menu. Single bonds can be changed to Double or Triple by left-clicking on them.

Templates

MarvinSketch provides several predefined chemical structures, called templates (e.g., cyclopenthane, cyclohexan, benzene). The templates can be accessed via the Advanced Templates Toolbar or through the Insert > Template Library menu.

1. Select a template using the Template Library or the Advanced Templates Toolbar area.

2. Place the template structure by left-clicking on the desired location.

Coordination compounds

• arrow between two atoms,
• dashed line between an atom and a group of atoms
.

To draw a coordinate bond between an atom and a group of atoms.

1. Select the atoms to be represented at one end of the coordinate bond by a multi-center.
2. Choose "Structure/Add/Multi-center" from the main menu or "Add/Multi-center" from the contextual menu. A multi-center represented by a "*" will be added. If you move the cursor to the multi-center the represented atoms are highlighted (blue circle around the atom labels).
3. Draw a coordinate bond from the multi-center and edit the other end of the bond if required. The "*" representing the multi-center disappears after bond drawing.
4. Repeat steps 2-4 to draw further multi-centers and coordinate bonds if required.

Markush structures

Position variation (Variable point of attachment)

To draw a position variation

1. Draw the structure that will include the position variation.
2. Select the alternative connecetion point atoms.
3. Choose "Structure/Add/Multi-center" from the main menu or "Add/Multi-center" from the contextual menu. A multi-center represented by a "*" will be added. If you move the cursor to the multi-center the represented atoms are highlighted (blue circle around the atom labels).
4. Draw a bond from the center and edit the bond if required. The represented atoms are displayed with grey shadow after this step. The "*" representing the multi-center disappears after bond drawing.
5. Repeat step 2-4 to draw further variable points if required.

Frequency variation (repeating unit with repetition ranges)

Reactions

How to Draw Reactions

You can place a reaction arrow on the canvas at any time, even on a blank canvas. Reaction errors are indicated by a red box around the reaction arrow. Only one reaction is allowed per molecule.

1. Select the React button. You will see the reaction arrow on the tip of the cursor when you move the mouse into the canvas area.

2. Click the location of the tail of the arrow.

3. Drag the mouse and release at the location of the head.

Once you have placed a reaction arrow on the canvas, MarvinSketch considers each part of the molecule in relation to the reaction. All parts of the molecule that are behind the arrow are considered reactants. Everything in front of the arrow is a product. Anything placed along the arrow is considered an agent. The validity of the drawn reaction will automatically be checked by Marvin. See Reactions for more information on using and disabling this feature.

How to Map Reactions

The arrow tool provides the easiest manual way to map corresponding reactant and product atoms. Select the arrow tool, hold down the left mouse button on a reactant atom, and drag it to the corresponding product atom. The same map number is added to both atoms marking, that they represent the same atom on the two sides of the reaction scheme. There are also keyboard shortcuts for mapping. Type m8, for example, and click on an atom. Atom map 8 is assigned to that atom.

Marvin contains an automapper tool as well (available from the Edit/Atom Mapping/Auto Map menu) assigning map numbers to all selected atoms of a reaction automatically.

Map numbers of the selected atoms can be removed by the Edit/Atom Mapping/Clear Map menu item, or by typing m0 for the selected atoms.

How to Draw R-group queries

An R-group query describes a set of derivatives in one query structure (substitution variation). It can be drawn the following way: First draw the root structure and place some R atoms either from the "More" dialog, from the popup menu or by typing a corresponding label such as "R1" on the keyboard. Then draw the variable R-group ligands and select those substituting the R1 atom. If you type "R1" now, the selected groups will be marked with "R1". Additional R-group conditions (Occurrence, RestH, If-then) can be set in the R-logic dialog available from the Edit/Attributes menu.

To draw the attachment points for the R-definitions, you can use menu "Group -> Attachment point" from the atom popup menu, or alternatively, when you draw the R-definitions and the mouse cursor still shows "R1", clicking on an atom of the definition will toggle the attachment point on that atom. (Please note that divalent R-groups must have two attachment points defined.)

Step by step example

1. Draw the root structure first.
   
2. Move the cursor to the atom where you would like to place the R-group. (In this example, we place R-groups in place of the terminal carbon atoms.) When the atom is highlighted (blue circle around the atom label), type the shortcut of the required R-group ID (e.g. R1). Alternative solution is selecting the ID from R-group sub-menu of the popup menu by pressing right mouse button over the atom.
   
3. Draw an alternative ligand with an R-group connection: Move the cursor to an empty place on the canvas (take care that nothing is selected) then press the shortcut of the next R-group (R2). The "in hand" object changes to the ID of the R-group (R2). (In this example, we add a ligand to terminal oxygen atom.) Move the cursor over the atom (the terminal oxygen) where you would like to add the new ligand and push the left mouse button. Then drag the mouse. You will see that the new bond is displayed and its orientation follows the cursor. Release the mouse button when the bond stands in the right direction.
   
4. Draw new fragments to the canvas (separately from the root structure), which will be the R-group definitions. (In this example, we draw the fragments for the first R-group definition to the right side and the second R-group definition will be placed below the root structure.)
   
5. Next, define the R-groups definitions. To do this, select those fragments that the first R-group should contain (on the right side). After the selection, press the shortcut of the R-group ID (R1). The ID and equal sign (R1=) will display beside the selected set and the "in hand" object will be the R-group ID.
6. Define attachment point to R-group members: Click the left mouse button on atoms where you would like place the attachment points. Repeat this operation on the other definitions of the R-group. (In this example, at the third definition, we select the left oxygen atom for attachment.) Alternatively, you can define R-group attachment points via the popup menu (by selecting Attachment point option from the Group menu on an atom of an R-group definition.
   
7. Create the second R-group by repeating the last two steps on the two remaining fragments.
   
8. You can define additional conditions, such as occurrence, rest H and if-then expressions to R-groups in the R-logic dialog. To do this, select menu option Edit -> Attributes -> R-logic. After setting the conditions in the R-logic dialog, press the OK button to apply the changes.
   

How to Draw S-groups

Abbreviated (superatom) S-groups

Syntax of the abbreviated S-group name

• \s - subscript
• \S - superscript
• \n - normal mode.

Multiple S-groups

Components, Unordered Mixtures and Ordered Mixtures

Ordered and unordered mixtures

Ordered mixtures, on the other hand contain ordered components, which define the order of addition. Example:

To draw an unordered component

1. Draw the structures that form the mixture.
2. To define a structure as a component in a mixture, first select the structure.
3. Choose "Create Group..." from the contextual menu (right mouse click on the selected structure).
4. In the "Create Group" dialog choose "Component (c)" from the "Type" combobox.
5. The "Order" field should be empty or should contain "none". If the "Order" field already contains a number, just delete it (you can type in "none" as well).
6. Click OK.

To draw an ordered component

1. Draw the structures that form the mixture.
2. To define a structure as a component in a mixture, first select the structure.
3. Choose "Create Group..." from the contextual menu (right mouse click on the selected structure).
4. In the "Create Group" dialog choose "Component (c)" from the "Type" combobox.
5. If this is the first component of the mixture, click the "Order" field and enter "1" in place of "none". If the "Order" field already contains a number Marvin will automatically increment the "Order" field for subsequent components.
6. Click OK.

To draw a mixture

1. Create and select the components to form the mixture.
2. Choose "Create Group..." from the contextual menu (right mouse click on the selected components).
3. In the "Create Group" dialog choose the type ("Ordered mixture(f)" or "Unordered mixture(for)") from the "Type" combobox.
4. Click OK.

To change the type of a mixture

1. Select the mixture to change the type.
2. Choose "Ungroup" from the contextual menu (right mouse click on the selected mixture).
3. Change the type of the included components.
4. Select the components to create the new mixture.
5. Create the new mixture from the selected components.

To add a new component to a mixture

1. Select the mixture to add the new component.
2. Choose "Ungroup" from the contextual menu (right mouse click on the selected mixture).
3. Create the new component to add.
4. Select the new and old components and create a mixture again.

To delete a component from a mixture

1. Select the mixture to delete the component from.
2. Choose "Ungroup" from the contextual menu (right mouse click on the selected mixture).
3. Delete the component.
4. Select the remaining components and create a mixture again.

Polymers

Source-based representation of polymers.

To draw a repeating unit select the atoms you want to be included and choose Create Group from Structure menu or Group/Create Group from contextual menu.

Structure-based representation of polymers.

• Polymers with two crossing bonds. If the polymer has one crossing bond on each bracket of the SRU there are three possibilites for the repeating pattern:
  • head-to-tail
  • head-to-head
  • either/unknown

  

• Ladder-Type Polymers Polymers with paired brackets and with two crossing bonds on each bracket are called ladder-type polymers. Here it must be specified how the two crossing bonds on each bracket connect to the corresponding bonds of the adjoining repeating units. Additionally to the head-to-tail, head-to-head connectivity information there is a flip information to specify whether the repeating unit flips around the polymer backbone when it connects to the adjoining SRU. These informations are handled only in case of brackets with exactly two crossing bonds on both side (head and tail side). We differentiate the following polymer connectivities:
  • head-to-tail with no flip
  • head-to-tail with flip
  • head-to-head with no flip
  • head-to-head with flip
  • either/unknown
  
  
• Polymers with three or more brackets. If the polymer has three or more bonds with a separated bracket on each bond, the polymer always has the either/unknown repeating pattern.

Copolymers

• random(ran)
• alternating(alt)
• block with or without junction unit (blk)
• copolymer to represent modified polymers (mod)
• copolymer to represent grafted polymers (grf)
• copolymer to represent cross-linked polymers (xl)

To draw a simple polymer

1. Draw the structure that forms the polymer.
2. To define a structure as a polymer, first select the structure. Leave out the atoms that should be replaced by "*" (star atoms).
3. Choose "Groups/Create Group..." from the contextual menu (right mouse click on the selected structure).
4. In the "Create Group" dialog choose the appropriate type from the "Type" combobox.
5. Set the polymer repeat pattern if neccessary.
6. Click OK. The star atoms ("*") will be added automatically.

To draw a ladder-type polymer

1. Draw the structure that forms the polymer.
2. To define a structure as a polymer, first select the structure. Leave out the atoms that should be replaced by "*" (star atoms).
3. Choose "Groups/Create Group..." from the contextual menu (right mouse click on the selected structure).
4. In the "Create Group" dialog choose the "SRU polymer" type from the "Type" combobox.
5. Set the polymer repeat pattern if neccessary.
6. Click OK. The star atoms ("*") will be added automatically.
7. To create a bracket that crosses two bonds select the two bonds (they should be already crossed by a single bracket each) and choose "Groups/Merge Brackets" from the contextual menu.

To draw a copolymer

1. Create and select the components to form the copolymer.
2. Choose "Groups/Create Group..." from the contextual menu (right mouse click on the selected components).
3. In the "Groups/Create Group" dialog choose the type ("Copolymer (co)", "Copolymer, alternating (alt)", "Copolymer, block (blk)" or "Copolymer, statistical (stat)") from the "Type" combobox.
4. Click OK.

To change the type of a polymer

1. Select the polymer to change the type.
2. Choose "Ungroup" from the contextual menu (right mouse click on the selected polymer).
3. Create the new polymer from the selected structure(s).

To add a new subpolymer to a copolymer

1. Select the copolymer to add the new subpolymer.
2. Choose "Ungroup" from the contextual menu (right mouse click on the selected copolymer).
3. Create the new subgroup to add.
4. Select the new and old subpolymers and create a copolymer.

To delete a subgroup from a copolymer

1. Select the copolymer to delete the subpolymer from.
2. Choose "Ungroup" from the contextual menu (right mouse click on the selected copolymer).
3. Delete the subpolymer.
4. Select the remaining subpolymers and create a polymer again.

Repeating units with repetition ranges

Syntax of the repetition ranges

To draw a repeating unit with repetition ranges

1. Draw the structure that forms or contains the repeating unit.
2. To define a part of the structure as a repeating unit, first select the part of the structure expected to repeat.
3. Choose "Groups/Create Group..." from the contextual menu (right mouse click on the selected part).
4. In the "Create Group" dialog choose the type "Repeating unit with repetition ranges" from the "Type" combobox.
5. Set the repetition ranges.
6. Click OK.

How to Draw Graphic Objects and Text Boxes

To draw a (poly)line, rectangle or text box, use the Insert menu. Point the mouse to the desired position on the canvas, click and hold the left button, move the mouse and release the button. After placing a text box, you can immediatelly use the keyboard to type a text.

To change the contents of a text box, choose Select mode, click on the box, then use the keyboard.

The shape of an object is changeable or resizeable by dragging one of its points to do it.

To insert the IUPAC Name text box choose it from the Insert menu, it will be automatically inserted under the structure. The name will be updated real-time.

How to Draw a Link atom

You can draw link atoms using the popup menu in two ways:

1. Right-click on the atom to bring up the popup menu. Select the required repetition number from the "Link node" submenu. Marvin will find out the outer (non-repeating) bonds for you.
2. Select the atom you would like to be the link node and two neighbouring bonds for outer (non-repeating) bonds. Right-click anywhere on the canvas to bring up the popup menu. Select the required repetition number from the "Link node" submenu.

Marvin will advise you if it is not possible to create a link node for the specified configuration (for example at ring fusions).

Outer (non-repeating) bonds will be denoted by brackets crossing them, and the repetition numbers will be put on the atom. All portion of the molecule connected to the link atom through non-outer bonds are supposed to repeat together with the atom. See examples below.

Molecule with link node	Meaning

To edit a link node repetition number or change outer bonds, repeat the drawing steps above. To make a link atom ordinary atom again, select "Off" from the "Link node" submenu.

How to Select a Structure

1. Set Selection mode on by clicking the Select button.

   1. To select a single atom, click on it.

   2. To select two joined atoms, click on the bond that links them.

   3. To select a rectangular region, click at one corner of the desired region and drag the mouse to the opposite corner. While the mouse button is pressed down, a guide will be displayed to aid you.

   4. To select a non-rectangular region, use the lasso select function.

      1. Click anywhere on the canvas and release the mouse button.

      2. Draw the region with your mouse (leaving all mouse buttons unpressed). A blue guide line will appear where you have drawn. A pink line will connect the start and end points.

      3. When you have finished drawing the region, click the mouse. In the event that you have not closed the region, the pink line will be used to close it for you.

You can unselect all by clicking an empty area of the canvas.

How to Delete a Structure

Using the Erase button:

1. Set Erase mode on by clicking the Erase button.

   1. To erase a single atom or bond, click on it.

   2. To erase a rectangular region, click at one corner of the desired region and drag the mouse to the opposite corner. While the mouse button is pressed down, a guide will be displayed to aid you.

   3. To select a non-rectangular region, use the lasso erase function.

      1. Click anywhere on the canvas and release the mouse button.

      2. Draw the region with your mouse (leaving all mouse buttons unpressed). A blue guide line will appear where you have drawn. A pink line will connect the start and end points.

      3. When you have finished drawing the region, click the mouse. In the event that you have not closed the region, the pink line will be used to close it for you.

Using Selection mode:

1. Select a portion of the structure.

2. Click the Cut button or use the DELETE button on your keyboard.

Using pop-up menus:

1. Right click on an atom or bond.

2. Select Remove from the pop-up menu.

How to Work with Structures

Visually Editing the Structure

You can edit a molecule using the methods described in How To Draw Structures and How To Delete A Structure.

Editing the Source

You can alter a molecule by directly editing its source in the Edit Source Window. You can view and edit the source in any of the supported file formats. To change format, simply select the desired one from the View Menu. To reload the molecule described by the text in this window into the MarvinSketch canvas (including any changes you may have made), select File > Import. This will close the Edit Source Window.

Cleaning

Marvin allows you to clean your molecule in either 2D or 3D. Cleaning will calculate new coordinates for the atoms. Generating conformers and choosing the favored one is also supported (in the Swing version). You can initiate cleaning via the Edit > Clean submenu. For more information on molecule cleaning, please visit this link.

Aromatic Rings

You can toggle the display of rings as aromatic using the Edit > Bonds submenu.

Structure Display Options

There is a wide range of functions related to the display of the molecules. These settings can be found in the View menu and the Preferences dialog. Additionally, you can move, rotate, and zoom in/out on the structure.

Moving and Rotating

You can move or rotate a selected structure.

1. Select the part of the structure you wish to move.

1. Moving the selection:

1. Move the mouse pointer toward the center of the selected structure until a blue rectangle appears.

2. Translate the selection by dragging the mouse.

2. Rotating the selection:

1. Move the mouse pointer toward the "edge" until a blue gear appears.

2. Rotate the selection by dragging the mouse.

Scaling

You can set the magnification of the molecule being on the canvas by the Zoom buttons. When a molecule is loaded into the sketcher it is scaled automatically to fit the window.

Molecule Format

You can set the display format for the molecule and screen resolution using the View > Display submenu. Available molecule formats are Wireframe, Wireframe with Knobs, Sticks, Ball and Stick, and Spacefill. You can set the resolution to low or high via the Quality submenu.

Colors

The View >Colors submenu allows you to specify the color scheme of the molecules. The available options are:

• Monochrome

• CPK

• Shapely - based on RasMol's shapely color scheme for nucleic and amino acids

• Group - based on PDB residue numbers

• Atom Set

Implicit/Explicit Hydrogens

Marvin has a number of options for the display of implicit and explicit hydrogens. Because Marvin is chemically intelligent, it will automatically add hydrogens as necessary within the structure. Generally, these will be implicit and displayed based on the options set in the View menu.

To view all hydrogens explicitly, displayed as atoms with bonds to neighbors, chose Edit > H-Atoms > Add. The Edit > H-Atoms > Remove will return to the previous display mode.

To view implicit hydrogens by symbol, use the View > Hydrogens > Implicit menu group. This option is disabled in Spacefill and Ball & Stick display modes.

Error Highlighting

Marvin can not automatically correct all valence errors or any reaction errors. Instead, these errors are highlighted and you may make the appropriate corrections yourself. This option can be enabled and disabled through the the Edit > Preferences box.

Saving Display Options

Many of the display settings in Marvin are saved and reloaded the next time you start the program. Background color, molecule color scheme, and hydrogen visibility can be set from the View menu and will saved automatically when you exit the program. Other options, including look & feel, error highlighting, and object visibility can be set using the Preferences dialog from the Edit menu.

Launching Other Windows

2D and 3D Viewer Windows

Choosing View >Open 2D Viewer or Open 3D Viewer launches a MarvinView window containing the current molecule from the Sketcher.

Sketcher Window

How to customize structure drawing styles

To load or define styles use the Edit > Format... menu. This menu brings up the "Format of the current document" dialog in which atom and bond format options can be specified. These include atom font type, size, color and bond thickness, color. All these options can be collectively set using styles. The top three radio buttons specify the target of the format settings being edited in the dialog. The "Apply changes for all the atoms/bonds" option allows to load predefined styles or to create your own style using the Load Style and Save Style buttons.

Loading a style

Saving a style

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