Customizing MarvinSketch

MarvinSketch can be customized to meet the needs of vastly different users.

As there are many different options, the customization process can get confusing. This section describes every option that affects the behavior of MarvinSketch in any way.

The table below lists all these options along with a short description and a link to the specific part of the MarvinSketch User's Guide that describes the option in detail. The table also provides information about where specific functions can be found on the GUI and which file is affected if an option is changed.

MarvinSketch stores all changes made on the GUI in various configuration files.

These files are located under one of the following folders:

  • USER_HOME/CHEMAXON_DIR

  • USER_HOME/CHEMAXON_DIR/VERSION

  • USER_HOME/CHEMAXON_DIR/journal_styles

  • USER_HOME/CHEMAXON_DIR/textstyles

The USER_HOME is C:\Documents and Settings\USERNAME on Windows and /home/USERNAME on Unix.

CHEMAXON_DIR is chemaxon on Windows and .chemaxon on Linux.

VERSION is the actual version number of MarvinSketch, with which the customization is made.

Example location:

  • Windows:
    C:\Documents and Settings\USERNAME\chemaxon\18.24.0\customization.xml

  • Unix/Linux:
    /home/USERNAME/.chemaxon/18.24.0/customization.xml

Name

Place on GUI

Short description

Associated sections

Associated files

Customizations that affect the whole GUI

Editor Style

View > Editor Style

There are three pre-defined styles in MarvinSketch. These are as follows:

  • Marvin

  • Marvin 5.0

  • View Mode

It is possible to edit these pre-defined styles and export them as needed.

It is also possible to import customized editor styles from XML or SER files.

The following aspects are customizable:

  • Menus

  • Popups

  • Toolbars

  • Keymap

Configurations of MarvinSketch

Menus Tab

Popups Tab

Toolbars Tab

Keymap Tab

Special Commands

CHEMAXON_DIR/VERSION/customization.xml

CHEMAXON_DIR/VERSION/shortcuts.xml

Hide/Show Status bars

View > Menu bar

The visibility of the Menu bar can be turned on or off.

Basic changes

Not persistent between sessions

Hide/Show Menu bars

View > Status bar

The visibility of the Status bar can be turned on or off.

Not persistent between sessions

Hide/Show Toolbars

View > Toolbars

In the case of the toolbar, the visibility of each toolbar can be specified individually.

These toolbars are as follows:

  • General

  • Chemical

  • 3D editing

  • Simple Templates

  • Advanced Templates

  • Search Online

  • Markush

  • Tools

  • Atoms

CHEMAXON_DIR/VERSION/customization.xml

Look and Feel

From file only

The general look and feel can be changed by adding a line to the marvin.properties file.

Changing the Default Look and Feel

CHEMAXON_DIR/marvin.properties

Customizations that affect the canvas

Color of the Canvas

View > Colors > Background

The color of the canvas can be changed to a specific color. The default color is white.

View Menu in MarvinSketch

CHEMAXON_DIR/marvin.properties

View > Colors > White Background

Changes the color of the canvas to white.

CHEMAXON_DIR/marvin.properties

View > Colors > Black Background

Changes the color of the canvas to black.

CHEMAXON_DIR/marvin.properties

Add Grid to the Canvas

View > Grid

Toggles the visibility of the grid.

CHEMAXON_DIR/marvin.properties(in 20.5.0 and later)

Add Guidelines to the Canvas

View > Guidelines

Toggles the visibility of the moveable guidelines.

Not persistent between sessions

Document-specific settings

Multipage Settings

File > Multipage Settings

Creates a multipage molecular document that helps to work with large drawings by dividing them into pages.

In the case of multipage documents, the following parameters can be specified:

  • Document Grid

  • Document Size

  • Margins

Multipage Documents

Not persistent between sessions

Document Style Settings

File > Document Style > Settings

By using this option, you can specify the font settings and size settings of the document.

The Font Settings consist of the atom font style and atom font size options.

Under Size Settings the following parameters are available:

  • Document Unit

  • Bond Length

  • Wireframe bond thickness

  • Bold bond width

  • Bond spacing

  • Hash spacing

  • Margin

The options above can be specified individually. Alternatively, you can choose from one of the pre-defined Journal Styles or create your custom style.

Customizing Structure Drawing Styles

CHEMAXON_DIR/marvin.properties

Custom styles:

CHEMAXON_DIR/journal_styles/styles.properties

CHEMAXON_DIR/journal_styles/CUSTOM_STYLE.properties

Expanding pre-defined lists/groups

Template Library

Edit > Template Library

Several pre-defined template groups are available in the Template Library. You can add entirely new groups to this list and modify the groups that are already added.

To add a new group, click Add Template Set and specify the path of the file that contains the set.

To remove a group, click Remove Template Set when a group is selected.

You can easily reorder the groups with the up and down arrows. It is also possible to specify some Advanced Templates bar options, for example, the maximum number of buttons on the bar or the size of the buttons.

When you switch to the Properties tab of a group you can specify whether the group is visible on the Advanced Templates bar or not.

Template Library Manager

CHEMAXON_DIR/marvin.templates.properties

My Templates

N/A

Any structure can be added to the user's template list. Simply select a structure and click Add to My Templates in the context menu.

CHEMAXON_DIR/marvin.mytemplates

Abbreviated Groups

You can create a user.abbrevgroup file to store your custom abbreviated groups.

Abbreviated (Superatom) Groups

CHEMAXON_DIR/user.abbrevgroup

Global preferences

Bond

Edit > Preferences

Bond-related behavior can be specified on this tab.

Bonds tab

CHEMAXON_DIR/marvin.properties

Structure

Structure-related behavior can be specified on this tab.

Structure tab

CHEMAXON_DIR/marvin.properties

Text

Text-related behavior can be specified on this tab.

Text tab

CHEMAXON_DIR/textstyles/text_styles.properties

CHEMAXON_DIR/textstyles/default.properties

Checkers

Checker-related behavior can be specified on this tab.

Checkers tab

CHEMAXON_DIR/checkerconfig.xml

Service

Service-related behavior can be specified on this tab.

Services tab

CHEMAXON_DIR/servicesconfig.xml

Save/load

Save and load related behavior can be specified on this tab.

Save-Load tab

CHEMAXON_DIR/marvin.properties

3D Options

3D-related behavior can be specified on this tab.

3D Options tab

CHEMAXON_DIR/marvin.properties

Analysis Box

Analysis box related behavior can be specified on this tab.

Analysis box tab

CHEMAXON_DIR/marvin.properties

Structure and object display customization

Structure Display

View > Structure Display

The following structure display styles are available:

  • Wireframe

  • Stick

  • Ball and Stick

  • Spacefill

Structure Display

CHEMAXON_DIR/marvin.properties

Color Schemes

View > Colors

The following color schemes are available:

  • Monochrome

  • CPK

  • Shapely

  • Group

  • Atom/Bond Sets

  • Peptide Colors

Color Schemes

CHEMAXON_DIR/marvin.properties

Implicit Hydrogens

View > Implicit Hydrogens

The following display modes are available:

  • Off

  • On Heteroatoms

  • On Heteroatoms or Terminal

  • All

Display Options for Implicit and Explicit Hydrogens

CHEMAXON_DIR/marvin.properties

Peptide Display

View > Peptide Display

The following options are available:

  • 1-letter

  • 3-letter

View Menu in MarvinSketch

CHEMAXON_DIR/marvin.properties

Atom Numbering

View > Advanced > Atom Numbering

The atom numbering scheme can be specified. The following options are available:

  • Off

  • Atom Numbers

  • IUPAC Numbering

Not persistent between sessions

Atom Properties

View > Advanced > Atom Properties

Toggles the visibility of atom properties.

Not persistent between sessions

Atom Mapping

View > Advanced > Atom Mapping

Toggles the visibility of atom mapping labels.

Not persistent between sessions

Bond Lengths

View > Advanced > Bond Lengths

Toggles the display of bond lengths in Angstroms in the middle of the bonds.

Not persistent between sessions

Lone Pairs

View > Advanced > Lone Pairs

Toggles the display of lone pairs.

Not persistent between sessions

R-groups

View > Advanced > R-groups

Toggles the display of R-group definitions.

Not persistent between sessions

R-Logic

View > Advanced > R-Logic

Toggles the display of R-logic definitions.

CHEMAXON_DIR/marvin.properties

Valence

View > Advanced > Valence

Toggles the display of valence numbers. The default setting is On.

Not persistent between sessions

Ligand Error

View > Advanced > Ligand Error

Toggles the display of ligand errors. The default setting is On.

Not persistent between sessions

S-group Attachments

View > Advanced > S-group Attachments

Toggles the display of the attachment points. The default setting is On.

Not persistent between sessions