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.

Tick the Show preview checkbox to see the contents of the file (molecules, reactions, queries). A single item is displayed in the preview window, the text field at the bottom shows the index of the current structure and the number of structures in the file. When a multiple structure file is selected (e.g. sdf), the navigation buttons become active. Their functions are: go to first, go to previous, go to next, go to last. Note, that this is not the selection which structure to open, it allows you only to check whether this is the file you would like to open.

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.

Pasting pictures with the help of OSRA is also possible (since version 5.3.0), please consult this page for details.

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 shrunken 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 status bar 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 status bar and the items in the View > Pages menu are available only if the Multipage document checkbox is set. The status bar contains information about the current page number in a text field 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 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 window, 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.
   In case of metals, the following rules apply: metallic elements from the 1st and 14-16th groups are added hydrogens, other appear as simple elements as default.
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.

Note: bold single bond type is functionally equal to the single bond. You might want to use it when drawing rings in perspective view.

Example:  

Templates

MarvinSketch provides several predefined chemical structures, called templates or structure templates (e.g., cyclopenthane, cyclohexane, benzene). They are categorized to template groups like Amino Acids, Polycyclics, etc.
The following template groups are available in MarvinSketch by default:

• Generic
• Rings
• Amino Acids
• Aromatics
• Bicyclics
• Bridged Polycyclics
• Crown Ethers
• Cycloalkanes
• Hetero Cycles
• Polycyclics
• Homology Groups
• My Templates

The templates can be accessed via the Advanced Templates Toolbar or through the Insert > Template Library menu.

Steps of drawing with templates:

1. Select a template using the Template Library or the Advanced Templates Toolbar area.
2. In case the template structure contains any S-groups, the group(s) can be optionally expanded or contracted by pressing the Shift button.
3. Place the template structure by left-clicking on the desired location.

Sprouting

Atom sprouting:

1. Click an atom symbol on the toolbar or periodic system.
2. Place the cursor over the atom where you would like to add the atom.
3. Press the Shift key on the keyboard then click the atom. The new atom will be attached to that atom.

Template sprouting: you can add the template connected by a bond formed between the selected non-primary atom and the attachment point of the template. This way adding a substituent will only replace a hydrogen atom on the selected atom, not the atom itself. This feature is limited to the use of symmetrical templates where attaching the template has only one possibility (e.g. as for phenyl).

1. Select a template from the toolbar or the template library
2. Move the cursor to the canvas and hover over an atom, a grey colored image will show you the position of the template.
3. Click the atom to place the template.

To change the connection type (no sprouting):

1. Select a template from the toolbar or the template library.
2. Move the cursor to the canvas and hover over an atom.
3. Press the Shift key and while holding it down, click the atom.

Adding a cyclohexane template to a secondary carbon atom:
Adding a cyclohexane template to a secondary carbon atom while holding down the Shift key:

Notes:

1. Abbreviated groups will be extended when holding down the Shift key, its attachment is not affected in terms of sprouting.
2. The grey outlined template will not be shown if the creation of a new bond would lead to the valence error of the atom but will be added if you click the atom.

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 connection 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)

Flip a molecule

Horizontal flip
Vertical flip

Horizontal Flip, Vertical Flip

Flip a selection:

1. Select part of the structure.
2. Right-click on the structure or go to Edit > Transformation menu.
3. Click on the command.

Flip the whole structure without selection:

1. Go to the Edit > Transformation menu.
2. Click on the command.

Note: If no structure is selected, the right-click on the canvas will not offer the flip command.

Group Flip

The Group Flip operation rotates the selected group by 180° around an axis set on the bond connecting the selection to the rest of the molecule. Stereocenters in the molecules are retained, the wedge bond styles change to keep the stereo information.

Group flip

1. Select part of the molecule.
2. Right-click on the canvas and select Transformation > Group Flip; or go to the Edit > Transformation menu.
3. Select Flip > Group.

Mirror a molecule

Horizontal mirroring
Vertical mirroring

Mirror a selection:

1. Select part the molecule.
2. Right-click on the canvas or go to the Edit > Transformation menu.
3. Click the command.

Mirror the whole structure without selection:

1. Go to the Edit > Transformation menu.
2. Click on the command.

Reactions

How to Draw Reactions

You can place a reaction arrow on the canvas at any time, even on a blank canvas. Only one reaction is allowed per molecule.

1. Select the Insert Reaction Arrow 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 before the arrow are considered reactants. Every molecule after the arrow is a product, and the ones placed along the arrow are considered agents.

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 as Structure > Reaction > Map Atoms) assigning map numbers to all selected atoms of a reaction automatically.

Map numbers of the selected atoms can be removed by the Structure > Reaction > Unmap Atoms 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 Periodic System dialog window, 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 window available from the Structure > 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 window. To do this, select menu option Structure > Attributes -> R-logic. After setting the conditions in the R-logic dialog window, press the OK button to apply the changes.
   

How to draw groups

You can create a group easily from a structure. There are two possibilities:

• Select the molecule or part of the molecule. Click the Create Group button in the toolbar and edit the group properties in the dialog window.
• Click the Create Group button in the toolbar then select parts of the group. Upon releasing the mouse button, the Group dialog pops up.

Edit groups: (since version 5.3) right-click on the group, select Edit group from the contextual menu and the group dialog opens.
Alternatively, select the group atoms and select Edit Group from the structure menu, Group submenu.

Abbreviated (superatom) groups

• Insert an abbreviated group into your sketch: type the name of the abbreviation, to complete a longer name, press ENTER or END after typing the first few characters. If the cursor was placed over an atom, it will be automatically changed to the abbreviated group. If no atom was selected, the abbreviation is placed on the cursor. Click on the canvas to place it. If you would like to ungroup an S-group before placing it to the canvas, press the SHIFT button before you release the mouse on the desired location.
• Create an abbreviated group: Click the Create Group button in the toolbar then select parts of the group. Upon releasing the mouse button, the Group dialog window pops up (this dialog window may be opened from the Structure > Group submenu as well). Name the group in the dialog window.

You can retrieve the hidden structure from the text abbreviation with the "Expand" function and hide the structure with the "Contract" function. Manipulation with abbreviated groups is possible with "Expand", "Contract", "Ungroup", and "Remove" from the Group submenu.

A short animation about abbreviated groups: Expand and ungroup abbreviated groups.

Add the abbreviated group to the Templates

After creating the abbreviated group (see previous section), right-click the corresponding atom and click to add the attachment point marked by an asterisk. This way you define the connection point of this group. Then select the group, right-click and press Add to My Templates. The template can be inserted by typing its name and clicking on the canvas.

Syntax of the abbreviated group name

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

Multiple 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, click the Group tool on the toolbar, then select the structure.
3. In the "Create Group" dialog window choose "Component (c)" from the "Type" list.
4. 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).
5. 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, click the Group tool on the toolbar, then select the structure.
3. In the "Create Group" dialog window choose "Component (c)" from the "Type" list.
4. 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.
5. Click OK.

To draw a mixture

1. Create the components to form the mixture.
2. Click the Group tool on the toolbar, then select the structures.
3. In the "Create Group" dialog window 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. Hover the mouse over the group.
2. Choose "Edit Group" from the contextual menu (right mouse click on the selected mixture).
3. Change the type of the mixture.
4. Click OK.

To add a new component to a mixture

1. Draw the new component.
2. Drag one part of the bracket and move it to enclose the new component.

To delete a component from a mixture

1. Select the component.
2. Press the Delete button on your keyboard or select the Erase tool.

Polymers

Source-based representation of polymers

To draw a repeating unit, click the Group tool on the tooolbar, then select the atoms you want to be included.

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 possibilities 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 flip information to specify whether the repeating unit flips around the polymer backbone when it connects to the adjoining SRU. These types of information 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. Click the Group tool on the toolbar, and select the structure. Leave out the atoms that should be replaced by "*" (star atoms).
3. In the "Create Group" dialog window choose the appropriate type from the "Type" list.
4. Set the polymer repeat pattern if necessary.
5. Click OK. The star atoms ("*") will be added automatically.

To draw a ladder-type polymer

1. Draw the structure that forms the polymer.
2. Click the Group tool on the toolbar, and select the structure. Leave out the atoms that should be replaced by "*" (star atoms).
3. In the "Create Group" dialog window choose the "SRU polymer" type from the "Type" list.
4. Set the polymer repeat pattern if necessary.
5. Click OK. The star atoms ("*") will be added automatically.
6. To create a bracket that crosses two bonds select the two brackets each crossing a bond and click Merge Brackets in the contextual menu.

To draw a copolymer

1. Create the components to form the copolymer.
2. Click the Group tool on the toolbar then select the components to be included.
3. In the "Create Group" dialog window choose the type ("Copolymer (co)", "Copolymer, alternating (alt)", "Copolymer, block (blk)" or "Copolymer, statistical (stat)") from the "Type" list.
4. Click OK.

To change the type of a polymer

1. Hover the mouse over the group.
2. Choose "Edit Group" from the contextual menu (right mouse click on the selected mixture).
3. Change the type of the polymer.
4. Click OK.

To add a new subpolymer to a copolymer

1. Draw the subpolymer to add outside of the bracket.
2. Drag one part of the bracket to include the new subpolymer. The new molecule should be marked with blue circles when you hover the mouse cursor over it.

To delete a subgroup from a copolymer

1. Select the subpolymer to delete.
2. Press the Delete button on your keyboard or with the Erase tool.

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. Click the Group tool on the toolbar, and select the structure.
3. In the "Create Group" dialog window choose the type "Repeating unit with repetition ranges" from the "Type" list.
4. Set the repetition ranges.
5. Click OK.

Charge of the group

Four types of groups can be assigned a charge sign: generic, component, monomer and mer groups. During group creation, you have the option to display the charge on the charged atom itself or the whole group. In the latter case, the charge will be displayed outside of the bracket on the right. If any additional charges are added (negative or positive) the net charge will be calculated and displayed. The charge-bearing atom can be revealed by pointing the cursor over the group (in select mode). To replace the charge, select the group and go to the Structure menu, Group submenu and click Edit Group (or right-click the selected group, and select Edit Group).

How to Draw Graphic Objects and Text Boxes

To draw a (poly)line, rectangle or text box, use the Insert menu or the toolbar (if visible). These objects are depicted in blue color outlines to indicate that any object here does not bear any chemical meaning like reaction arrows or S-group brackets (in black). Point the mouse to the desired position on the canvas, click and hold the left button, move the mouse and release the button. To create a small rectangle or text box click again. After placing a text box, you can immediately 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 resizable 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 neighboring 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 one of the three available Selection buttons.
   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, choose Rectangle Selection, 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, choose Lasso Selection, press the left mouse button to start selecting, and draw the region with your mouse without releasing the mouse button. A blue guide line appears along the selection region. A pink line will connect the start and end points.
   5. To select a fragment
      • double-click on an atom or bond using Rectangle or Lasso selection,
      • or use the Structure Selection button and single-click on an atom or bond.

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 selection function first, then press the Erase button.

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 As. If the automatic format recognition detects a file format (checking it by a priority list), it will be offered in the Select Import Mode field (Import as Recognized, indicating the file type in brackets). If the structure is associated to a file type of higher priority than your choice, choose the Import As option to set the file format.
For example, you want to create the seryl-asparagine dipeptide: write "SN" in the Source, then select Import. The automatic option detects it as SMILES, but if you select the Import As option, and then the "Peptide Sequence" from the list, it will be imported correctly.
In addition, there are some cases when the automatic recognition cannot detect the file format, even though the entered text is correct (although it is very rare). In this case the Import As Recognized option is disabled and you have to choose the format from the list of the Import As option.

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. You can initiate cleaning via the Structure > Clean2D/3D submenu. For more information on molecule cleaning, please visit this link.

Submenus

• Clean 2D
  • Clean in 2D: cleans the molecule(s) in 2D
  • Hydrogenize Chiral Cneter: adds an explicit hydrogen with a wedge bond to chiral centers which have no terminal atoms as substituents
  • Clean Wedge Bonds: changes wedge bonds for convention display
• Clean 3D
  • Clean in 3D: cleans the molecule(s) in 3D
  • Cleaning Method: choosing from various methods
  • Display Stored Conformers: works only if conformers of the sketched molecule had been generated with the help of the Conformer plugin, choosing the 'Store conformer information in property field' option. See details in the plugin's documentation.

Aromatic Rings

You can toggle the display of rings as aromatic using the Structure > Aromatization 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 window. Additionally, you can move, rotate, and zoom in/out on the structure.

Moving and Rotating

You can move or rotate a selected structure.

First, 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.
      (You can also use the Space key to change between transformation modes.)

   2. Translate the selection by dragging the mouse.

2. Rotating the selection:

   1. Move the mouse pointer toward the outline of the molecule until a blue gear appears.
      (You can also use the Space key to change between transformation modes.)

   2. Rotate the selection by dragging the mouse.

3. Rotating the selection in 3D:

   1. Use the Space key 3 times to select this rotation mode.

   2. Rotate the selection in 3D by dragging the mouse.

• Note: currently 3D coordinates of brackets (e.g. monomer, component type groups) are not correctly updated when rotating the molecule in 3D mode. Avoid when possible.

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 Structure > Add > Add Explicit Hydrogens. The Structure > Remove > Remove Explicit Hydrogens will return to the previous display mode.

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

Displaying the label of carbon atoms

Displaying the label of carbon atoms in structures is possible the following way:

• Always - Always show the atom labels of carbon atoms.
• Never - Never show the atom labels of carbon atoms.
• At straight angles and at impl. Hs - Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.

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 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 be saved automatically when you exit the program. Other options, including look & feel, error highlighting, and object visibility can be set using the Preferences dialog window 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 of MarvinSketch.

How to customize structure drawing styles

More advanced display format can be obtained for the molecule by applying format styles. Format styles in Marvin include the setting of the following attributes:

• type of atom font,
• size of atom font,
• color of atoms,
• thickness of bonds,
• color of bonds.

When loading a molecule all atoms/bonds belong to the default atom/bond set if no styles were applied previously. After selecting an atom/bond set and applying a style for it, the selected atoms/bonds are removed from the default atom/bond set and a new set is created from the atoms/bonds with new style. All the atoms/bonds, whose style were not yet modified by selection and applying a style on them, still belong to the default atom/bond set.

Your changes might be applied for a set of atoms/bonds:

• for the selected atom/bond set,
• for the default atom/bond set,
• for all the atoms/bonds.

Loading a style

Saving a style

Set the "Structure Drawing Properties" you wish to save and press the Save Style button to get to the "Save" dialog where you can enter the name of the style file and save the style. All your own saved files will be stored under the <HOMEDIR>/chemaxon/styles/ directory (where <HOMEDIR> is the user's home directory) and will be added to the combobox items. A new style file can be added to the chemaxon/marvin/styles directory under the Marvin installation directory. This new style file has to be listed in file chemaxon/marvin/styles/styleFileList.properties. The new style file will be copied to the <HOMEDIR>/chemaxon/styles/ directory and appear in the combobox of the "Loading of a journal style" dialog. (No existing style files under <HOMEDIR>/chemaxon/styles/ are overwritten)

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