Dialogs of MarvinSketch

Contents

• Customize
• Preferences
• Edit Source
• Format
• Periodic Table
• Template Library Manager
• Create Group
• Attach data
• Document Settings
• About MarvinSketch

Customize

The Customize dialog window, located in the View > Editor style menu, provides options for altering the user interface by adding, removing, or reorganizing its elements. For a detailed description, please consult this page.

Preferences

The Preferences dialog window is located at the Edit menu. It allows you to change many of the MarvinSketch display settings, including error highlighting and object visibility.
All settings are saved and used when the application is restarted.

Display

• Atom & Bond labels are used as the default font type and size to labels such as C/T label of bonds, atom query property labels of atoms, etc.
• Double bond spacing is a gap between two lines/sticks representing a double or triple bond measured in Angstroms.
• Wireframe bond thickness is the width of bonds in wireframe mode. It is measured in Angstroms.
• Stick diameter is the width of bonds in stick mode in Angstroms.
• Ball radius is the size of atom spheres in Ball draw type, measured in Angstroms.
• MarvinView Layout sets the default layout to Automatic, Molecule matrix or Spreadsheet.
• Show Bond in Hand when checked, bond types are shown under the mouse cursor like template structures.
• 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.
• Circled Charge labels are used as the font type and size of the circled charge symbols.
• Fog effect factor: manual setting of the fading strength. No fog: all regions of the structure is displayed with the same line strength and color. Strong effect: the fading is at its maximum (molecule is only slightly visible at the far end).

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.
• Any Bond Line Style offers three different modes to display bonds of unknown types: Automatic, Dashed and Solid. This option can be separately set to be used in MarvinSketch and MarvinView.
• Terminal Bond Deletion Method offers 2 ways to delete the terminal bond of a molecule: only the bond is deleted or the terminal atom disappears with the bond.
• "Coordinate" Bond Line Style allows changing the type of coordinate bonds from the default ones (arrow for single atom and hashed for multicenter) to solid.

Structure

• Highlighting Valence Errors highlights atoms having wrong valences with 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.
• Validate S-groups At Creation disables the S-group types in the drop-down list which would not yield a chemically correct structure. Usage in MarvinSketch.
• Carbon Labels options determine the condition of displaying C labels on Carbon atoms.

  Always	Never	At straight angles and implicit H atoms

• Ligand Orders
  • Always
  • Never
  • On R-groups with definitions

Checkers

• Move up/down the checker items: the fixing process may depend on the sequence of the checkers. Checking order can be set using the Up/Down buttons on selected checkers.
• Add checkers to the list: the default list can be modified by adding other checkers.
• Remove checkers from the list: the default list can be modified by removing checkers not needed.
• Open checker configuration from URL open a checker configuration from URL.
• Open checker configuration: open your custom checker configuration from file.
• Save checker configuration: save your custom checker configuration to file.
• Configure external checkers/fixers: add external checkers/fixers; save or load external checker/fixer configuration.

Services

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 service(s) can be used from the Tools > Services menu afterwards.

• Set the order of services by moving them up and down using the Up/Down buttons.
• Add a new service to the list by the add button. The preference window of the new service will pop up. Read more about setting different services.
• Remove the selected service from the list by the remove button.
• Open Service Configuration from URL. Specify a previously set configuration of services with its URL.
• Import Service Configuration from file. Import a previously set configuration XML file.
• Export Service Configuration to file. You can export the set services to a configuration XML file.

Save/Load

• Default location: the folder from which to load or to save molecules may be set by the user.
  • Startup directory: the folder where the command to start the application was given.
  • Last location: the last folder used for opening or saving a structure.
  • Custom working directory: a user-defined folder. If a molecule is loaded from another folder, then the file's location will be offered for saving.
• Default file format determines which type is offered by default when structures are saved to file.
• Save/Load settings
  • Save/Load GUI settings (.MRV, .PDF format) allows storing and loading of display options like background color, font type, stereo labels, atom indices etc. in addition to the chemical structure itself. This option can only be used with MRV and PDF formats.
  • 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' dropdown list on the General Toolbar is supplemented with 'Scaffold' and 'R1, R2, R3...' only when there are defined R-group(s). Without R-group definitions the zooming scale for the loaded structure(s) will not be modified, the last zooming scale will be used.
    When this option is switched off in the 'Preferences' menu then MSketch opens the new file with the last zoom level.
• 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 URL of a server on which a chemical structure recognition program runs can be given.
• Name import service URL URL of a server on which a chemical name recognition program runs can be given.

OLEServer

Edit Source

You can alter a molecule by directly editing its source in the Edit Source dialog window.
The dialog window provides standard clipboard operations and it is also possible to send the source text to the console.
You can view and edit the source in any of the supported file formats. You can also convert it to Java String which allows easy integration of the structure to a custom Java application code.
To change the format of the source, simply select one from the View Menu. If there are more than one molecule on the canvas, setting View as multiple molecules in the View Menu causes each molecule to appear in a separate block in the source. This feature works only in those cases where the selected format is able to handle multiple fragments.

After editing the source text, you can send the structure back to the MarvinSketch canvas by invoking File > Import As, and pressing Import on the appearing dialog window. This will close the Edit Source dialog window.

Format

Atoms and Bonds

On this panel there are many options to change the drawing properties of atoms and bonds.

For more information about using structure drawing styles, please visit this link.

Graphics Objects

The drawing properties of graphics objects (text boxes, brackets, lines, etc.) can be changed on this panel.

Periodic Table of Chemical Elements

Periodic Table

Chemical elements are available as buttons on the Periodic Table panel of MarvinSketch.
Atom buttons are arranged according to the standard periodic table layout.
When the mouse cursor is over a specific atom button, the information panel displays the name of the atom, the atomic number, mass, electronegativity and the oxidation states.
When one of the atom buttons is pressed, the corresponding atom can be placed on the canvas. The atom symbol appears under the mouse cursor, while the button is highlighted in this case.

The Atom List and NOT List buttons can be used to create special atom lists that can be used in queries. When one of these buttons is pressed, atoms can be added to the list by pressing atom buttons one after the other. The lists are not cleared when the list buttons become unselected. The atoms of the list are also shown under the mouse cursor above the canvas. See Query Guide for more details about atom lists and not lists.

Four different coloring schemas can be chosen:

1. CPK: colors the atoms according to the Corey-Pauling-Kultun coloring scheme
2. Standard state: colors according to the standard state of the element (gas, liquid, solid)
3. Blocks: colors elements according to the highest-energy electron's orbital (s-, p-, d- or f-block)
4. Metals/Nonmetals: colors according to the metallic character of the elements (alkali, alkaline earth, metalloid, transition metal, other metal, nonmetal)

Advanced

For the meanings of the buttons on the Advanced tab please refer to the Query Guide.
When the mouse cursor is over a button, a short description appears on the information panel.

Generic query atoms

Atom query properties

Periodic Table Groups

Special nodes

R-groups

Custom Property

Template Library Manager

The Template Library is a hierarchic display of template sets.

It contains several template sets by default (such as Generic, Rings, Amino Acids, etc), and a special set called My Templates.

Template Options

• Maximum number of molecules: template sets can contain large number of molecules. This option maximizes the number of structures being loaded from a template set when it is selected in the Template Library. For example if the option is set to 100, only 100 structures will be loaded to memory and displayed in the library, even if the underlying molecule file contained 25000 structures.
• Coordinates: this option is to specify an operation affecting the coordinates when the templates are placed on the canvas.
  For example result of placing L-Alanine to the canvas with different options:

  As in the original structures	Always perform Clean2D	Always perform Clean3D

• Size of templates: the size with which each template is displayed in the library, measured in pixels.
• Maximum number of buttons: this determines the maximum number of buttons allowed on the Advanced Templates Toolbar

Adding a new template set to the library

It is also possible to specify a location with ftp protocol. The underlying subdirectories and files will be displayed as with the local file system.

Please note that protocols other than file and ftp are not supported. However remote file systems can help to overcome this restriction.

Removing a template set from the library

Create Group

• Anypolymer (anyp)
• Component (c)
• Copolymers
• Crosslink (xl)
• Generic ()
• Graft
• Mer (mer)
• Modification (mod)
• Monomer (mon)
• Multiple group
• Ordered mixture (f)
• Repeating units with repetition ranges
• R-group
• SRU polymer(n)
• Superatom (abbreviation)
• Unordered mixture (mix)

Attach data

Attached data is a custom field assigned to atoms or brackets. It has an identifier string (name) and a value. Furthermore, a query operator can describe different restrictions in queries.
The dialog provides interface to set the properties of such a field.

Further details of attached data can be found in the Query guide.

Attaching data in MarvinSketch is described here.

The Attach Data dialog is customizable; configuration options and a small example can be found here.

Edit properties

Properties may be added and viewed in MarvinSketch. Various properties can be added, but the value is displayed only on the canvas. Detailed description

Document Settings

About MarvinSketch