How to Use Basic MarvinSketch Functions

Reactions

How to Draw Reactions

You can place a reaction arrow on the canvas at any time, even on a blank canvas. Please note that only one reaction arrow can be placed on the whole canvas.

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. You can align and/or distribute the objects of the reaction scheme by selecting the relevant option in Edit > Object menu. The centers of the objects will be considered during the alignment/distribution of objects. Note that selected agent fragments and texts are moved together with the arrow while keeping the distance between them.
Once the reaction arrow has been placed on the canvas, MarvinSketch automatically puts plus signs between reactant and product molecules. If you wan to avoid having plus signs between specific reactants and/or products, you have to select the relevant fragments and use the Structure > Reaction > Merge Reactants (Products) menu option. If you want to remove one or more molecules from such a merged item, select the relevant molecules and go to Structure > Reaction > UnmergeReactants (Products).

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. Similar tool "Manual Atom Map" can be added by customization. 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 > Mapping > 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 > Mapping > Unmap Atoms menu item, or by typing m0 for the selected atoms.

How to Draw Electron Flow Arrows

Electron flow arrows show the actual direction of motion of the electrons. They can point from an electron or lone pair of an atom or from a bond to another atom or bond or even to an incipient bond (formed after the electron transition).

1. Select the arrow type (single electron flow or electron pair flow). (Menu: Insert > Electron Flow)
2. Move the cursor over a bond, electron, or lone pair (or over the atom itself if the valence electrons are not displayed around it) of the structure on the canvas, and push the mouse button. (It will be the source of the electron flow.)
3. Select the destination: drag the arrow while holding down the mouse button and release the button over the destination to finalize the electron flow arrow.

Query Structures

There are molecules that cannot be represented by a single structure. Although it is possible to run multiple structure searches in cascade, it is much more efficient to run a search only once using a well designed query structure. This structure often contains query features, possibly including complex conditional expressions for atoms and bonds. For a more detailed description of this please see the Query Guide.

The easiest way to use Query Atoms, different Query Groups and Query Atom Properties is to find them on the Periodic Table's Advanced tab.

Atom Lists and NOT Lists

It is possible to define the type of an atom in a custom atom list. If the type of the corresponding atom in the target molecular structure is a member of the list, it is considered a matching atom. NOT lists can be used to specify atoms to be excluded in the search.

"Atom List" and "NOT List" can be reached from the Periodic Table's Periodic Table dialog.

Custom Properties

Values can be added to the following "Custom Property" types from the Periodic Table's Advanced tab.:

R-group Converts the atom to an R-group with an index of the input "Value". (Only numerical values are allowed, with a maximum number of 32767.) This atom can be used to describe an unknown or unspecified molecule part or to draw an R-group query or a Markush structure.

Alias Converts the Alias value to the atom label. The input of the textbox is displayed as the atom label, but the atom itself does not change.

Pseudo Converts the input of the textbox "Value" to Pseudo atom type. The input of the textbox is displayed as the atom label, but the atom is replaced by an "Any" type Query atom.

SMARTS Converts the input of the textbox "Value" to a complex SMARTS query molecule or atom. If the cursor is kept over the canvas during typing, the conversion can be seen on-the-fly.

Value Adds the input of the textbox "Value" to the atom as its "Atom Value" property.

Homology Groups

'Built-in' Homology groups can be found in the 'Special Nodes' section of the Periodic Table's Advanced tab, as a dropdown list, starting with "Alkyl".

More deatils of some other Query features and Homology groups are in the Query Guide.

R-group Query

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 Table 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, that can be reached from the Structure > Attributes menu item. More details can be found here.

To draw the attachment points for the R-definitions, you can use menu Atom > R-group Attachment from the menu (or R-group Attachment from the 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.)

How to draw R-group queries -- 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 'R1' (or the other required R-label) on the keyboard. Alternative solution is selecting the R-label from R-group sub-menu of the popup menu by pressing right mouse button over the atom. You can replace selected atoms by R-labels using the list either on the Advanced tab of the Periodic Table or in the Atom > R-group menu item.
   
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 type the next R-group label (R2 in this case). The "in hand" object changes to the ID of the R-group (R2). (In this example, we add a ligand to terminal oxygen atom.) Click the terminal oxygen, 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 separately from the root structure, which will belong to one of the two 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-group definitions. To do this, select those fragments that the first R-group should contain (on the right side). After selection, type the first R-group ID (R1) on the keyboard. The ID and equal sign (R1=) will be displayed beside the selected set and the "in hand" object will be the R1-label.
6. Define attachment points on R-group members: Click with the left mouse button on atoms where you would like to place the attachment points. Repeat this operation on the other two members in the R1-definition. (In this example, at the third molecule, we select the left oxygen atom for attachment.) Alternatively, you can define R-group attachment points via the popup menu by selecting the R-group attachment option on an atom of an R-group definition.
   
7. Create the R2-definition by repeating the last two steps on the two remaining fragments.
   
8. In case of one attachment point, the connections are not numbered, only marked by a wavy line on the substituent side.
   In case of more than one attachment point, the connections are marked by numbers on the root structure (the so called ligand order). Connection points on the substituents are marked with a wavy line, and the order is indicated by numbers (except for the first one).
   
9. The ligand order on a bond can be changed using the Bond > Ligand order menu item. Simply select the bond in question and go to this menu option (also available upon mouse-over in the context menu). Selecting another ligand order option in the offered list will transpose the two affected ligand order numbers. The example below demonstrates a case where we want to change ligand order on a bond which connects two R-groups.


10. 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.
    
    
    
    R-logic can be visualized by switching on the View > Advanced > R-logic menu option.

Markush structures

Position Variation (variable point of attachment)

• Draw the structure that will include the position variation.
• Select the alternative connection point atoms.
• 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).
• 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.
• Repeat step 2-4 to draw further variable points if required.

Frequency variation (Repeating unit with repetition ranges)

Homology groups in a Markush structure

The simplest way is to insert homology groups from the Periodic Table's Advanced tab.

1. Open the Periodic Table (toolbar or from the Atom menu), choose the Advanced tab.
2. In the Special nodes section, choose the homology group from the dropdown list.
3. The homology group stays at the mouse pointer, you can click the atom(s) on the canvas. You don't need to close the Periodic Table to continue drawing.

Editing the homology group properties in MarvinSketch

Select the homology group and right-click. Choose Edit Properties... Set the group properties in the dialog box.

Here is an example of the property dialog window for a cycloalkyl group:

By default, the atom and homology group properties are not shown. You can switch it on by checking the View > Advanced > Atom Properties menu.

How to Create 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.

Group types: In the dropdown list of the group type only those types are allowed which are enabled for the actual selection in the molecule (to enable all types: go to Edit > Preferences > Structure tab and uncheck the 'Validate S-groups at creation' box.)
Enabling/disabling a group type depends on:

• The number of crossing bonds it would have.
• The embedding of groups into each other: several conditions are checked here for the group to be created
  • whether it can be embedded into the groups which would contain it,
    e.g. polymer S-groups can not be embedded into multiple S-groups
  • whether it can embed all the groups which would be contained by it,
    e.g. structural repeating unit S-groups (SRU) can not embed monomers
  • whether it can be embedded directly into the group which would be its direct embedder,
    e.g. component S-groups can be directly embedded only into ordered or unordered mixtures
  • whether it can directly embed the groups which would be embedded by it directly,
    e.g. mixtures can directly embed only components.
• Expandable S-groups are not allowed to be embedded into each other.

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. Typing group abbreviations is case sensitive: e.g., typing either "NO" or "no" both lead to the nitrosyl (NO) functional group, while typing "No" results in the atom symbol of nobelium. 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 the group atoms and bonds. 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 attachment points to abbreviated groups

After creating the abbreviated group (see previous section), right-click the corresponding atom and choose "Add S-group attachment", or select the atom and use the same option in the Atom menu. The attachment point is marked by a number in a green rectangle. This way, you defined a connection point of this group. (Please note that attachment points can be added only to abbreviated groups, so it is important to define the group first.)
There is no limit to how many attachment points can be added to an abbreviated group; they will be numbered in the order of their creation. Crossing bonds will connect to group atoms through their first free attachment point. Only attachment points not occupied by crossing bonds are marked by numbers in the expanded abbreviated group. Similarly, crossing bonds connect to a contracted abbreviated group through the first free attachment point of the whole group.
Removal of an attachment point works the following way: Select the "Remove S-group attachment" option either from the pop-up menu or from the Atom menu to erase the attachment point with the highest number on the atom in question.
When you defined an abbreviated group, you can add it to the templates. 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.

User-defined abbreviated groups

Besides the default abbreviated groups you can also set up your own user-defined groups or redefine the default ones. Marvin stores its default groups in a formatted .txt file named default.abbrevgroup and by adding your own group file you can complement the default. To assemble your own .abbrevgroup file you should strictly follow abbreviated groups file format. The newly defined file must be named user.abbrevgroup and should be stored in the chemaxon folder of your home directory in your file system. Note that Marvin gives priority to the user-defined abbreviated groups and overrides the default after redefinition.

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.

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

After placing a text box, you can immediately use the keyboard to type a text. Symbols can be inserted directly through the Insert symbol tool, . The tool contains the list of the most commonly used symbols by default. This list will be updated according to your latest selections. Click on the relevant symbol and it will appear in the textbox. If the desired symbol is not on the list, click on More Symbols for the full character list.

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

You can place a text box with the IUPAC name(s) from the Structure > Structure to Name > Place IUPAC Name menu command and it will be automatically inserted under the structure. The name will be updated in 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. The deletion of the terminal bond deletes the terminal atom by default. Pressing the Alt button while deleting the bond, the terminal atom is not deleted. To change the default behaviour, go to Edit > Preferences > Bonds tab and choose the desired Terminal Bond Deletion Method.

   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. If there are multiple molecules on the canvas, checking View as multiple molecules in the View Menu leads to each molecule appearing in a separate block in the source. This feature works only, if the selected format is able to handle multiple structures.

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:

   Rotation in 3D of the following structural parts is possible:
   • all compounds on the canvas,
   • selected fragments,
   • selected groups.

   Rotation of all compunds on the canvas in 3D can be accomplished by the View > Mouse mode > Rotate in 3D menu option.
   The axis of the 3D rotation for selected objects can be determined in the Edit > Transform > Rotate in 3D menu (or from the contextual menu) by choosing from the following list:

   • Around an arbitrary axis defined by two atoms: in this case you are asked to select the atoms prior to the rotation.
   • Around x axis: horizontal axis in the plane of the canvas
   • Around y axis: vertical axis in the plane of the canvas
   • Around z axis: axis perpendicular to the plane of the canvas
   • Free 3D rotation: the rotation follows the movement of the mouse (click&drag).
     (Note: 3D rotation mode until version 5.3.x: pressing the Space key 3 times initiates the free 3D rotation.)
   • Group Rotate: available only for a selected group in a molecule. The connecting bond(s) is recognized between the selected and unselected parts of the structure and selects the rotation axis accordingly.

   The rotations are visualized by the fog effect: parts of the molecule behind the canvas are of lighter colour than the parts on the canvas. To see best the 3D view, use white background (View > Colors > White Background).

4. Customized tool: 3D plane:

   1. Select 3 atoms in the molecule.

   2. Click the 3D Plane button or select Edit > Transformation > 3D Plane. The selected 3 atoms will lie in the plane of the canvas. The coordinates are changed, not only the view of the structure.

• 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

Set the magnification of the molecule on the canvas by the Zoom buttons. If you have a mouse with a wheel, hold down the Ctrl key, and then scroll the wheel to zoom in or out. When a molecule is loaded into the sketcher, it is scaled automatically to fit the window.

Individual objects (bonds, reaction arrows, graphical objects, text boxes) or sets of objects can be scaled, too. Selecting these objects, corners of a bounding rectangle will appear. Dragging one of these corners, the selection will be scaled proportionally. In case of bond scaling, the percentage of the current bond length relative to the default value will be visible. The same result can be achieved by opening the Format... dialog either through the File > Document Style option or from the pop-up menu.

Molecule Format

You can set the display format for the molecule and screen resolution using the View > Structure 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 > 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 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,
• length 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

After pressing the Load Style button, you can load a style from a combo box or browse amongst the previously defined style files. The chosen style will be loaded into the "Structure Drawing Properties" in the "Format of the current document" dialog.

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 chemaxon/styles/ directory of your 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 chemaxon/styles/ library in your home directory and appear in the combobox of the "Loading of a journal style" dialog. (Existing style files will not be overwritten.)

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