H_off

Do not show implicit Hydrogen labels.

H_hetero

Implicit Hydrogen labels on heteroatoms only.

H_heteroterm

Implicit Hydrogen labels on hetero- and terminal atoms (default).

H_all

Implicit Hydrogen labels on all atoms.

chiral_off

Switch off chirality support, do not show R/S labels (default).

chiral_selected

Show R/S if the chiral flag is set for the molecule.

chiral_all

Show R/S for any molecule.

noRGroups

Do not show R-groups.

noRLogic

Do not show R-logic.

w...
h...

Image width and height in pixels. If only one from w and h is specified, then the other will have the same value. If none of them is specified, then their values are calculated from scale. If scale is not specified, then the default size is 200x200.

scale...

Magnification. 1.54Å (C-C bond length) is scale pixels.

maxscale...

Maximizes the magnification to prevent overscaling of small molecules.
It is usually set to 28, which is the scale factor for 100% magnification.

atsiz...

Atom label font size in C-C bond length units. Default: 0.4

Note: atsiz*1.54 Å = atsiz*scale points

atomFont...

Atom label font type and size in pt.

Examples:
atomFont:SansSerif-ITALIC-10
atomFont:Times New Roman-PLAIN-10

bondl...

Bond length in pt. Default: 28

Example: bondl42.0

bondw...

Width of double bond in C-C bond length units. Default: 0.18

Note: bondw*1.54 Å = bondw*scale pixels

boldbondw...

Width of bold bond in pt. Default: 6

bondHashSpacing...

The spacing of the hash in hashed bonds in C-C bond length units.

wireThickness...

Bond thickness in wireframe mode. Default: 0.064

stickThickness...

The stick diameter for ball and stick mode. Default: 0.1

ballRadius...

Ball radius for ball and stick mode. Default: 0.5

#rrggbb

Background color. It also determines the brightness of the CPK palette (for atoms and bonds); lighter colors are choosen automatically for dark background and conversely. Default: "#ffffff"

#aarrggbb

Background color with alpha value. Use alpha=0 for transparent background, e.g. "#00ffffff". Note that the alpha channel is not supported by all image formats. Default: "#ffffffff"

transbg

Sets the image background to transparent.

mono

Black & white.

cpk

Use CPK colors (default).

shapely

Use the shapely color scheme.

group

Use coloring based on residue sequence numbers.

setcolors:...

Use atom/bond set colors. Colors can be specified as a colon separated list of values. Use "ak:#rrggbb" for atom set k, "bk:#rrggbb" for bond set k. The hashmark "#" can be omitted. Human-readable color names like "red", "green", "blue" can also be used.

wireframe

Wireframe rendering style (default for 2D).

wireknobs

Wireframe with knobs - used til version 17.9. Later versions fall back to wireframe

ballstick

"Ball & stick" rendering style (default for 3D).

spacefill

Spacefill rendering style.

noantialias

Switch off antialiasing.

amap

Displays atom mapping.

anum

Displays atom numbers.

atomNumberingType...

Sets the type of atom numbering. Implies anum parameter.
Possible values:

• 1 (Atom numbers)

• 2 (IUPAC numbering)

lp

Displays lone pairs.

lpexpl

Display the explicit lone pairs instead of the implicit lone pairs if lone pair displaying is switched on. See the lp parameter.

lonePairsAsLine

Display lone pairs as a line instead of the default two dots. This parameter has effect only if the lp parameter is also specified.

downwedge_mdl

Down wedge orientation points downward (MDL). (default)

downwedge_daylight

Down wedge orientation points upward (Daylight).

anybond_auto

Draw any bonds with dashed lines in most cases. If all bonds are generated from atom coordinates, any bonds are displayed with solid lines. (default)

anybond_dashed

Draw any bonds with dashed lines.

anybond_solid

Draw any bond with solid lines.

noatsym

Hide atom symbols in 3D mode.

valprop

Show valence property on atoms that have the valence property explicitly set.

ez

Show E/Z labels.

cv_on

Always show the atom labels of carbon atoms.

cv_off

Never show the atom labels of carbon atoms.

cv_inChain

Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.

bondLengthVisible

Display the length of bonds in Angstroms.

valenceErrorVisible

Display valence errors.

absLabelVisible

Set the Abolute label visibility to true.

ligandOrderVisibility_withDef

Active by default. Show ligand order on images only when the R-group definition is present.

ligandOrderVisibility_on

Show all ligand order on images for R-groups.

ligandOrderVisibility_off

Never show ligand order on images for R-groups.

aprop

Show explicitly set properties on atoms.

liganderr

Show ligand errors on R-groups.

coordBondStyle_solid

Display coordinate bond as a single bond.

coordBondStyle_arrow

Display coordinate bond as an arrow.

coordBondStyleAtMulticenter_hashed

Display coordinate bond as a dashed bond when it connects to a multicenter atom.

coordBondStyleAtMulticenter_solid

Display coordinate bond as a single bond when it connects to a multicenter atom.

chargeWithCircle

Display charge symbols in a circle.

oneLetterPeptideDisplay

Display peptides with their one letter abbreviation instead of the three letter abbreviation which is the default.

disableAminoAcidBondColoring

Disable the amino acid bond coloring.

fogFactor...

Set the fog factor scale value (integer). Default value: 0, range: 0..100.

marginSize...

Set the margin width in pt. Default: 10

jpeg

Default settings: 200x200 pixels, white background (or black in 3D).

jpeg:w100,#ffff00

100x100 JPEG with yellow background.

jpeg:w100,h150

100x150 JPEG with default background.

png:aprop -s "C1-C10 alkyl" -o alkyl.png

PNG showing "C1-C10 alkyl".