Structure Display

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Under this option group you can define style and chemistry related properties of displayed structures.



Structure Display options


After changing structure display and scaling options in Options dialog, these changes can be applied by selecting a single structure and pressing one of the following buttons, respectively: "Display", "Scale", "Display and Scale":




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


You can check the whole process on the following video:



Color Scheme

The color scheme of displayed structures can be selected here:



Allow No Structure

This option is used when you click on Add or Edit button in ribbon, leave the structure editor empty and click OK. If the option is set to True, after clicking OK, "No structure" text will be displayed in the document/presentation/e-mail message. (The text string can be specified in a separate option: No Structure Text.) If the option is set to False, the structure box remains empty.


Atom Symbols Visible in 3D

Sets atom symbol visibility in 3D mode. Note that in 3D mode, atoms may become invisible in wireframe mode by hiding atom symbols.


No Structure Text

Here you can type in any kind of text you would like to see when you draw "No structure", which means that you opened the structure editor but didn't draw any atoms or bonds and clicked OK button.




Caffeine with Rendering  - Wireframe




Caffeine with Rendering  - Ball and Stick



Caffeine with Rendering – Spacefill                



Explicit Hydrogens

Sets the visibility state of explicit hydrogen atoms.

Note: The structure should contain explicit Hs for display.

Caffeine with Explicit Hydrogens


Implicit Hydrogens

It can be selected, which implicit hydrogens to be displayed:



Atom Mapping

Displays atom mapping (TRUE or FALSE).


Esterification reaction with mapped O atoms.


Atom Numbers

You can select from the following three options:

Off: no atom numbers will be displayed on the structures.

AtomNumbers: atom numbers will be ordered as in Marvin.

IUPACNumbering: atom numbers will be ordered according to IUPAC rules.


Numbering with AtomNumbers option

Numbering with IUPACNumbering option


Atom Properties Visible

Displays atom properties (TRUE or FALSE).


Bond Lengths Visible

Displays bond lengths (TRUE or FALSE).

Caffeine displayed with Bond Lengths


Graph Invariants

Displays graph invariants (TRUE or FALSE).

Caffeine displayed with Graph Invariants


Lone Pairs

Displays lone pairs (TRUE or FALSE).

Caffeine with Lone Pairs displayed



If this option is set to TRUE (default value), R-group definitions are visible beside Markush or scaffold structures containing R-groups, if it is FALSE, R-group definitions are hidden.


Valence Errors

Displays valence errors in the structure (TRUE or FALSE).

Quaternary ammonium ion with no charge


Preferences – Bonds




Any Bond Line Style

It can be selected, how to display bonds with unknown order:



Aromatic Bonds As Discrete Double Bonds (TRUE or FALSE)

Displays the aromatic structures in Kekule format (discrete double bonds instead of the aromatic rings). Default value is TRUE.


Coordinate Bond Style

Sets the coordinative bond line style (arrow or solid) when both atoms are single.


Coordinate Bond Style at Multicenter

Sets the coordinative bond line style (hashed or solid) when one of the atoms is a multicenter.


Down Wedge Orientation

Sets the wedge bond display convention

Down wedge points downward in MDL's convention, upward (at the chiral center) in Daylight's.


Preferences – Display




In case of these options positive values can be added or in some cases zero. If you add negative values, they will automatically turned to the default value.


Atom Font Type

The font type for atoms in drawn structures can be specified here. The list consists of available font types depends on the regional settings of your operational system, the default is Microsoft Sans Serif.


Atom Font Size

Sets atom label font size in points, the default value is: 11 pt.




Caffeine with default atom font size (11 pt) and 24 pt.


Ball Radius

Sets ball radius for ball and stick mode. Default value is: 0.5


clip0009        clip0010



Caffeine with default and 0.75 Ball Radius


Bold Bond Width (pt)


Sets the width of the line used when bold bond is drawn. The end of the wedge bonds is 1.5 times the bold width, the default is 5.


Bond Hash Spacing (pt)


Sets the spacing between the hashed lines for 'single down' wedged bonds and hashed bonds, the default is 2.7.


Bond Length (pt)

With setting the value of this option, it can be specified how long the bonds should be displayed in the cells or documents. Any positive number can be added as values. The default value is 28.


Carbon Labels

It can be selected, which carbon labels should be displayed:

Caffeine with Carbon Labels: Never

Caffeine with Carbon Labels: Always


Charge with Circle

Displays the charge on molecules in a circle if it is set to True, and without a circle if it is set to False.


Double Bond Width (pt)

Sets the width of double bonds in points. Default value is: 4 pt.




Caffeine with default double bond width (4pt) and with 10 pt.


Margin Size (pt)


Sets the space surrounding the bundle rectangle.


Stick Thickness

Sets the stick diameter for ball and stick mode. Default value is: 0.1.


clip0004        clip0006


Caffeine with default 0.1 and 0.2 Stick Thickness


Wire Thickness (pt)

Sets bond thickness in wireframe mode. Default value is: 1.2.




Caffeine with default 1.2 and 2.4 Wire Thickness



Absolute Labels (TRUE or FALSE)

Sets the visibility state of absolute stereo configuration labels.

Structure displayed with absolute stereo configuration label


E/Z Labels (TRUE or FALSE)

Sets the visibility state of absolute double bond stereo configuration labels.

Structure displayed with absolute stereo double bond configuration label


R/S Labels

This option has 4 possible values (see also in Marvin Sketch's User's Guide):

Structure displayed with R/S labels



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