Structure Display Options in JChem for Excel

    With these options, it is possible to define the style and chemistry-related properties of the displayed structures.

    For more information, see the Structure Display Options section of the MarvinSketch User's Guide.

    The figure below shows the structure display options of JChem for Excel.

    images/download/attachments/1806976/Structure_Display_Options.png

    Colors

    Color Scheme

    Use this option to specify the color scheme of the displayed structures.

    The following schemes are available:

    • Monochrome

    • CPK

    • Shapely

    • Group

    The default scheme is CPK.

    Display

    Allow No Structure

    This option affects cell behavior when you click Add/Edit and leave the canvas of the structure editor empty then click OK.

    By using this option, you can specify whether the No Structure text is added to cells after the scenario described above or not. When the text is added to the cell, the JCSYSStructure function is also created for the cell. You can specify the text string by using the No Structure Text option.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is TRUE.

    Atom Symbols Visible in 3D

    Use this option to specify whether atom symbols are visible in 3D mode or not.

    {info} Atoms may become invisible in wireframe mode when atom symbols are hidden.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is TRUE.

    No Structure Text

    Use this option to customize the text that is displayed when no structure is drawn to a cell.

    The default text is No Structure.

    Rendering

    By using this option you can specify the structure display style.

    The following styles are available:

    • Wireframe

    • Ball and Stick

    • Spacefill

    The default style is Wireframe.

    The table below shows the different styles.

    Style Wireframe Ball and Stick Spacefill
    Example images/download/attachments/1806976/Wireframe_Caffeine.png Caffeine Wireframe images/download/attachments/1806976/Ball_and_Stick_Caffeine.png Caffeine Ball and Stick images/download/attachments/1806976/Spacefill_Caffeine.png Caffeine Spacefill

    Hydrogens

    Explicit Hydrogens

    Use this option to specify the visibility of explicit hydrogen atoms.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    Implicit Hydrogens

    Use this option to specify the display mode of implicit hydrogens.

    The following display modes are available:

    • Off

    • On Heteroatoms

    • On Heteroatoms or Terminal

    • All

    The default display mode is On Heteroatoms or Terminal.

    The table below shows the different display modes.

    Display mode Off On Heteroatoms On Heteroatoms or Terminal All
    Example images/download/attachments/1806976/Implicit_Off.png images/download/attachments/1806976/Implicit_Hetero.png images/download/attachments/1806976/Implicit_Hetero_and_Terminal.png images/download/attachments/1806976/Implicit_On_All.png

    Misc

    Atom Mapping

    Use this option to specify whether atom mapping is shown or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is TRUE.

    Atom Numbers

    By using this option you can select from the following atom number displays:

    • Off: No atom numbers are displayed on the structures.

    • AtomNumbers: Atom numbers are ordered as in Marvin.

    • IUPACNumbering: Atom numbers are ordered according to IUPAC rules.

    The default display is Off.

    The table below shows the various display options.

    Display mode AtomNumbers IUPACNumbering
    Example images/download/attachments/1806976/Numbering_AtomNumbers.png images/download/attachments/1806976/Numbering_IUPACNumbers.png

    Atom Properties Visible

    Use this option to specify whether atom properties are displayed or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    Bond Lengths Visible

    Use this option to specify whether bond lengths are visible or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    Graph Invariants

    Use this option to specify whether graph invariants are displayed or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    Lone Pairs

    Use this option to specify whether lone pairs are visible or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    R-groups

    Use this option to specify whether R-group definitions are visible beside Markush or scaffold structures containing R-groups or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is TRUE.

    Valence Errors

    Use this option to specify whether valance errors are shown or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    Preferences – Bonds

    Any Bond Line Style

    By using this option, you can specify the display mode of bonds with unknown order.

    The following modes are available:

    • Automatic (in most cases, this means a dashed line, solid lines are only used when all bonds are generated from atom coordinates, for example, in the case of XYZ and PDB files).

    • Dashed

    • Solid

    Aromatic Bonds as Discrete Double Bonds

    Use this option to specify whether aromatic structures are displayed in Kekule format (discrete double bonds instead of the aromatic rings) or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is TRUE.

    Coordinate Bond Style

    By using this option, you can specify the line style of coordinative bonds when both atoms are single.

    The following styles are available:

    • Arrow

    • Solid

    The default style is Arrow.

    Coordinate Bond Style at Multicenter

    By using this option, you can specify the line style of coordinative bonds when one of the atoms is multicenter.

    The following styles are available:

    • Hashed

    • Solid

    The default style is Hashed.

    Down Wedge Orientation

    Use this option to set the display convention of the wedge bonds.

    The following displays are available:

    • Points Downward (MDL)

    • Points Upward (Daylight)

    The default display is Points Downward (MDL).

    Preferences – Display

    In the case of these options, when defining a numerical value use positive values (in some cases zero is allowed). A negative value is overwritten with the default value.

    Atom Font Type

    Use this option to specify the font type of atoms in the structures.

    The available types depend on the regional settings of your operating system. It is possible to use non-default Windows font types.

    The default style is Microsoft Sans Serif.

    Atom Font Size [pt]

    Use this option to specify the atom label font size in points.

    The default value is 10.

    Ball Radius

    Use this option to specify the ball radius for the ball and stick model.

    The default value is 0.5.

    Bold Bond Width [pt]

    Use this option to specify the width of the line (in points) used when a bold bond is drawn.

    The default value is 5.

    Bond Hash Spacing [pt]

    Use this option to specify the spacing between (in points) the hashed lines for single down wedged bonds and hashed bonds.

    The default value is 2.7.

    Bond Length [pt]

    Use this option to specify the length of bonds in points.

    Any positive number can be used.

    The default value is 28.

    Carbon Labels

    By using this option, you can specify how carbon labels are displayed.

    The following modes are available:

    • Always

    • Never

    • At straight angles and implicit H atoms

    The default option is A t straight angles and implicit H atoms.

    The table below shows the different modes.

    Display mode Always Never At straight angles and implicit H atoms
    Example images/download/attachments/1806976/Carbon_Always.png images/download/attachments/1806976/Carbon_Never.png images/download/attachments/1806976/Carbon_At_Straight_Angles_and_at_Implicit_H_Atoms.png

    Charge with Circle

    Use this option to specify whether charges on molecules are displayed in a circle or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    Double Bond Width (pt)

    Use this option to specify the width of double bonds in points.

    The default value is 5.

    Margin Size (pt)

    Use this option to specify the margin width of the bounding rectangle in points.

    The default value is 7.

    Stick Thickness

    Use this option to specify the stick diameter for the ball and stick model.

    The default value is 0.1.

    Wire Thickness (pt)

    Use this option to specify the bond thickness in points for the wireframe model.

    The default value is 1.2.

    Stereo

    Absolute Labels

    Use this option to specify whether the absolute stereo configuration labels are visible or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    E/Z Labels

    Use this option to specify whether the absolute double bond stereo configuration labels are visible or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    M/P Labels

    Use this option to specify whether the axial stereochemistry labels are visible or not.

    The available values for this option are as follows:

    • TRUE

    • FALSE

    The default value is FALSE.

    R/S Labels

    The table below lists all possible values for this option along with a description and the name of the corresponding MarvinSketch option.

    Option in JChem for Excel Description Option in MarvinSketch
    Switch off chirality support, do not show R/S labels No R/S labels are displayed. Stereo > R/S Labels > None
    Show R/S if the chiral flag is set for the molecule R/S labels are displayed if an absolute stereo (chiral) flag is added to the molecule. Stereo > R/S Labels > Absolute Stereo
    Show R/S for any molecule Shows R/S chirality for all atoms in the molecule. Stereo > R/S Labels > All
    Show all possible R/S for any molecule Atoms that could have an R/S stereo label—but it is not possible to decide which one exactly—are marked with a question mark. Stereo > R/S Labels > All possible

    For more information about these options in MarvinSketch, see View Menu.