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/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:


      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 ModeIt 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 MarvinSketchMenus TabPopups TabToolbars TabKeymap TabSpecial 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 file. Changing the Default Look and Feel CHEMAXON_DIR/
      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/
      View > Colors > White Background Changes the color of the canvas to white. CHEMAXON_DIR/
      View > Colors > Black Background Changes the color of the canvas to black. CHEMAXON_DIR/
      Add Grid to the Canvas View > Grid Toggles the visibility of the grid. CHEMAXON_DIR/ 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 * MarginThe 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/ Custom styles: CHEMAXON_DIR/journal_styles/ CHEMAXON_DIR/journal_styles/
      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/
      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/
      Structure Structure-related behavior can be specified on this tab. Structure tab CHEMAXON_DIR/
      Text Text-related behavior can be specified on this tab. Text tab CHEMAXON_DIR/textstyles/ CHEMAXON_DIR/textstyles/
      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/
      3D Options 3D-related behavior can be specified on this tab. 3D Options tab CHEMAXON_DIR/
      Analysis Box Analysis box related behavior can be specified on this tab. Analysis box tab CHEMAXON_DIR/
      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/
      Color Schemes View > Colors The following color schemes are available: Monochrome CPK Shapely Group Atom/Bond Sets Peptide Colors Color Schemes CHEMAXON_DIR/
      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/
      Peptide Display View > Peptide Display The following options are available: 1-letter 3-letter View Menu in MarvinSketch CHEMAXON_DIR/
      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/
      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