Structure Display

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Display

Rendering

       

Caffeine with Rendering  - Ball and Stick

 

Caffeine with Rendering – Spacefill                

 

Hydrogens

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: All, On Heteroatoms, On Heteroatoms or Terminal, or Off.

 

Misc

Atom Mapping

Displays atom mapping.

Atom Numbers

Displays atom numbers.

Caffeine with Atom Numbers displayed

Bond Lengths

Display bond lengths.

Caffeine with Atom Numbers displayed

Graph Invariants

Displays graph invariants.

Caffeine with Graph Invariants displayed

Lone Pairs

Displays lone pairs.

Caffeine with Lone Pairs displayed

Valence Errors

Displays valence errors in the structure.

Quaternary ammonium ion with no charge

 

Preferences – Bonds

Any Bond Line Style

It can be selected, how to display bonds with unknown order: Automatic, Dashed, Solid. Automatic means dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).

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.

Aromatic Bonds As Discrete Double Bonds

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

 

Preferences – Display

Atom Label Font Size

Sets atom label font size in C-C bond length units. Default value is: 0.4 [Atom Label Font Size]*1.54 Å

Caffeine with 0.8 Atom Label Size

Ball Radius

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

Caffeine with 0.75 Ball Radius

Carbon Labels

It can be selected the label of carbon atoms in structures to be displayed:

Always: Always shows the atom labels of carbon atoms.

Never: Never shows the atom labels of carbon atoms.

At straight angles and at implicit H atoms: Shows the atom labels of carbon atoms at straight angles and at implicit Hydrogens. This is the default option.

Caffeine with Carbon Labels: Never

Caffeine with Carbon Labels: Always

Double Bond Width

Sets the width of double bonds in C-C bond length units. Default value is: 0.18 [Double Bond Width]*1.54 Å = [Double Bond Width]*scale pixels.

Caffeine with 0.36 Double Bond Width

Stick Thickness

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

Caffeine with 0.2 Stick Thickness

Wire Thickness

Sets bond thickness in wireframe mode. Default value is: 0.064.

Caffeine with 0.28 Wire Thickness

 

Stereo

Absolute Labels

Sets the visibility state of absolute stereo configuration labels.

Structure with absolute stereo configuration label displayed

E/Z Labels

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

Structure with absolute stereo double bond configuration label displayed

R/S Labels

Sets the visibility state of R/S labels.

Structure with R/S labels displayed

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