Structure Display in JChem for Office

The same structure display options can be used in JChem for Office as in JChem for Excel. Changing an option and pressing OK on the Options dialog has an immediate effect in JChem for Excel.

In JChem for Word, Powerpoint, and Outlook, the Display, Scale, or the Display and Scale ribbon buttons must be used to refresh the structures.

Changes affect only a single structure in Word, Powerpoint, and Outlook but in Excel are structures are affected.

images/download/attachments/1802789/Display_Buttons.png

By pressing the Display and Scale button, both structure display and fixed scale options will take effect.

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.

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 At 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.