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
    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. Basic changes 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
    		 Basic changes 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
    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 CHEMAXON_DIR/marvin.properties
    Color of the Canvas View > Colors > White Background Changes the color of the canvas to white. View Menu CHEMAXON_DIR/marvin.properties
    Color of the Canvas View > Colors > Black Background Changes the color of the canvas to black. View Menu CHEMAXON_DIR/marvin.properties
    Add Grid to the Canvas View > Grid Toggles the visibility of the grid. View Menu CHEMAXON_DIR/marvin.properties(in 20.5.0 and later)
    Add Guidelines to the Canvas View > Guidelines Toggles the visibility of the moveable guidelines. View Menu Not persistent between sessions
    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
    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. Template Library Manager CHEMAXON_DIR/marvin.mytemplates
    Abbreviated Groups N/A You can create a user.abbrevgroup file to store your custom abbreviated groups. Abbreviated (Superatom) Groups CHEMAXON_DIR/user.abbrevgroup
    Bond Edit > Preferences Bond-related behavior can be specified on this tab. Bonds Tab CHEMAXON_DIR/marvin.properties
    Structure Edit > Preferences Structure-related behavior can be specified on this tab. Structure Tab CHEMAXON_DIR/marvin.properties
    Text Edit > Preferences Text-related behavior can be specified on this tab. Text Tab CHEMAXON_DIR/textstyles/text_styles.properties CHEMAXON_DIR/textstyles/default.properties
    Checkers Edit > Preferences Checker-related behavior can be specified on this tab. Checkers Tab CHEMAXON_DIR/checkerconfig.xml
    Service Edit > Preferences Service-related behavior can be specified on this tab. Services Tab CHEMAXON_DIR/servicesconfig.xml
    Save/load Edit > Preferences Save and load related behavior can be specified on this tab. Save-Load Tab CHEMAXON_DIR/marvin.properties
    3D Options Edit > Preferences 3D-related behavior can be specified on this tab. 3D Options Tab CHEMAXON_DIR/marvin.properties
    Analysis Box Edit > Preferences Analysis box related behavior can be specified on this tab. Analysis Box Tab CHEMAXON_DIR/marvin.properties
    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 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
    		 View Menu Not persistent between sessions
    Atom Properties View > Advanced > Atom Properties Toggles the visibility of atom properties. View Menu Not persistent between sessions
    Atom Mapping View > Advanced > Atom Mapping Toggles the visibility of atom mapping labels. View Menu Not persistent between sessions
    Bond Lengths View > Advanced > Bond Lengths Toggles the display of bond lengths in Angstroms in the middle of the bonds. View Menu Not persistent between sessions
    Lone Pairs View > Advanced > Lone Pairs Toggles the display of lone pairs. View Menu Not persistent between sessions
    R-groups View > Advanced > R-groups Toggles the display of R-group definitions. View Menu Not persistent between sessions
    R-Logic View > Advanced > R-Logic Toggles the display of R-logic definitions. View Menu CHEMAXON_DIR/marvin.properties
    Valence View > Advanced > Valence Toggles the display of valence numbers. The default setting is On. View Menu Not persistent between sessions
    Ligand Error View > Advanced > Ligand Error Toggles the display of ligand errors. The default setting is On. View Menu Not persistent between sessions
    S-group Attachments View > Advanced > S-group Attachments Toggles the display of the attachment points. The default setting is On. View Menu Not persistent between sessions