Preferences

The Preferences dialog window is available through Edit > Preferences.

In this window, you can change the display settings, error highlighting, and object visibility of MarvinSketch.ű The settings are saved and used when the application is restarted. You can restore the default settings by using the Restore Defaults button at the bottom of the window. This dialog window consists of the following tabs:

• Bonds Tab
• Structure Tab
• Text Tab
• Checkers Tab
• Services Tab
• Save-Load Tab
• 3D Options Tab
• Analysis Box Tab

Bonds Tab

Name	Description
Show Bond in Hand	When this box is checked, there is visual feedback when you select any of the bonds.
Down Wedge Orientation	Allows changing the wedge bond display convention. Down wedge points downward in MDL's convention, upward (at the chiral center) in Daylight's.
Terminal Bond Deletion Method	The terminal bond can be deleted in one of the following two ways: With the Terminal Atom: The terminal atom disappears with the bond. Without the Terminal Atom: Only the bond is deleted.
"Any" Bond Line Style	Select from the following modes for unknown bond type display: Automatic, Dashed, or Solid. The option can be separately set for MarvinSketch and MarvinView.
"Coordinate" Bond Line Style	Select the type of coordinate bonds from the following: Single Atoms, Arrow, Solid, Multicenter, Hashed, or Solid.

Structure Tab

Name	Description
Highlight Valence Errors	Highlights atoms having wrong valences with a red underline when it is checked.
Automatic Lone Pair Calculation	Calculates lone pairs automatically. Make sure View > Misc > Lone Pairs is checked to see the result.
Automatic Plus Signs in Single Step Reactions	Enables automatic reaction recognition.For more information, see Creating Reactions.
Validate S-groups At Creation	Disables the S-group types in the drop-down list which would not yield a chemically correct structure.For more information, see Substructure Groups in MarvinSketch.
Highlight Valence Errors	Highlights atoms having wrong valences with a red underline in MarvinView.
Show Lone Pair as Line	When checked, lone pairs on the canvas are shown as lines.
Show Charge in Circle	When checked, a circle is displayed around the charge.
Carbon Labels > Always
Carbon Labels > Never
Carbon Labels > At straight angles and implicit H atoms
Ligand Orders > Always	Always display the ligand order information for an R-group.
Ligand Orders > Always Never	Never display the ligand order information for an R-group.
Ligand Orders > Always On R-groups with definitions	Only display the ligand order information on R-groups with definitions.

Text Tab

By using the options available in this tab you can specify the default style of textboxes and analysis boxes.

The following options are available:

• Font
• Size
• Style
• Color
• Alignment

To modify the style of a specific textbox, select the textbox and navigate to Edit > Format or use the Advanced template toolbar. This can be used only for one selected textbox at a time.

Checkers Tab

Name	Icon	Description
Move up checker item		Moves checker up. The fixing process may depend on the sequence of the checkers.
Move down checker item		Moves checker down. The fixing process may depend on the sequence of the checkers.
Add checker to the list		Adds a checker to the list.
Remove checker from the list		Removes checker from the list.
Open checker configuration from URL		Opens a checker configuration from a URL.
Open checker configuration		Opens your custom checker configuration from a file.
Save checker configuration		Saves your custom checker configuration to a file.
Configure external checkers/fixers		Adds external checkers/fixers; saves or loads external checker/fixer configuration.

Services Tab

The Services Module provides seamless integration of third-party calculations into Marvin Sketch. You can add and configure the desired calculations in the Services tab. The set services can be used from the Services menu afterward.

Name	Icon	Description
Move up service		Moves the selected service up.
Move down service		Moves the selected service down.
Add service		Adds a new service to the list.
Remove service		Removes a service from the list.
Open service configuration from URL		Opens a previously set configuration of services from a URL.
Import service configuration from file		Imports a previously set configuration XML file.
Export service configuration to file		Export the set services to a configuration XML file.

Save-Load Tab

Name	Description
Startup Directory	Sets the folder from which to load or to save molecules to the directory from which the command to start the application was given.
Last Location	Sets the folder from which to load or to save molecules to the last folder used for opening or saving a structure.
Custom Working directory	Sets the folder from which to load or to save molecules to a user-defined folder.If a molecule is loaded from another folder, then the location of the file will be offered for saving.
Save/Load GUI Settings (.MRV, .PDF format)	Allows storing and loading of display options like background color, font type, stereo labels, atom indices, and so on, in addition to the chemical structure itself.This option can only be used with MRV and PDF formats and it is selected by default.
Save/Load Zoom Factor (.MRV format)	Stores and loads the zooming scale of the structures.This option can only be used with the MRV format.
Zoom to Scaffold on Load (Sketch only)	Sets the zooming scale to Scaffold if the loaded file contains defined R-groups, so the R-group definitions might not be seen on the canvas without scrolling.The Zoom level drop-down list on the General Toolbar is supplemented with Scaffold and R1, R2, R3 only when there are defined R-groups.Without R-group definitions, the zooming scale for the loaded structures will not be modified, the last zooming scale will be used.When this option is switched off in the Preferences menu, MarvinSketch opens the new file with the last zoom level.
Save BOM to New MRV and MDL Files	Saves Byte Order Mark (BOM) to new files.
Recent File Entries	Defines the number of files in the Recent files list in the File menu, with values between 1 and 10.
Image Import Service URL	Specify the URL of a server on which a chemical structure recognition program runs.
Name Import Service URL	Specify the URL of a server on which a chemical name recognition program runs.

3D Options Tab

Name	Description
Stick Diameter	Specifies the width of bonds in stick mode in Angstroms.
Ball Radius	Specifies the size of atom spheres in ball-draw type, measured in Angstroms.
Fog Effect Factor	Sets the fading strength. No fog: All regions of the structure is displayed with the same line strength and color. Strong: The fading is at its maximum (molecule is only slightly visible at the far end).
Fine Build	Fine Clean3D builds up conformers of fragments to find low energy conformers. Leaves failed fragments intact.
Fine with Hydrogenize	The build process always adds explicit Hydrogens to the structures which are removed if not present in the original molecule.This option prevents the removal of extra Hydrogen atoms, otherwise, it gives the same results as Fine Build.
Fast Build	Fast clean, which if fails, performs a fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.
Build or Optimize	Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.
Gradient Optimize	Optimizes with the Dreiding force field using the actual structure as starting geometry.

Analysis Box Tab

MarvinSketch can calculate some basic properties for your structures, which can be pasted into your drawing.

The calculations update upon modification except if they applied to a selection. For more information, see the Analysis Box. You can set the properties you want to be displayed and their order as well. The following properties can be calculated:

• Name
• Traditional name
• Molecular weight
• Formula
• Formula with charge
• Exact mass
• Dot-disconnected formula
• Dot-disconnected formula with charge
• Isotope composition
• m/z distribution

The decimals setting applies to the exact mass value only. By default, the value of molecular weight is set to three decimal places.