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ParameterMeaning 
absLabelVisibleShow (true) or hide (false) "Absolute" labelfalse
aminoAcidBondColoringEnabledEnable (true) or disable (false) peptide bridge coloringtrue
atomFontAtom symbol/label font: Serif, SansSerif or MonospacedSansSerif
atomMappingVisibleShow (true) or hide (false) atom mappingtrue
atomPropertiesVisibleShow (true) or hide (false) atom propertiestrue
atomNumbersVisibleDeprecated 
atomNumberingTypeSets the type of atom numbering to Off(0), Atom numbers (1) or IUPAC numbering (2)0
valencePropertyVisibleShow (true) or hide (false) valence propertiestrue
atomsizeAtom symbol font size in C-C bond length units:
atomsize*1.54 Å = atomsize*scale points, where scale is the current magnification.
0.4
atomSymbolsVisibleShow (true) or hide (false) atom symbols in 3D viewtrue
bondLengthVisibleShow (true) or hide (false) bond length labelsfalse
bondSpacingDouble bond spacing in C-C bond length units:
spacing*1.54 Å = spacing*scale pixels, where scale is the current magnification.
0.18
chargeWithCircleCharge label (plus or minus sign) is displayed circled(true) or normal(false)false
chiralitySupportWhen to show atom chirality (R/S).
  • off - never
  • selected - if the chiral flag is set for the molecule or the atom's enhanced stereo type is absolute
  • all - always
off
circledChargeFontCircled charge labels font: any of the fonts installed on the machine. Deprecated, will be removed by January 1st 2016.SansSerif
circledChargeSizeCircled Charge labels font size in C-C bond length units:
circledChargeSize*1.54 Å = circledChargeSize*scale points Deprecated, will be removed by January 1st 2016.
0.4
colorSchemeColor scheme.
  • mono - monochrome
  • cpk - Corey-Pauling-Kultun
  • shapely - shapely (residue types)
  • group - residue sequence numbers
cpk
downWedgeWedge bond display convention. Down wedge points downward in MDL's convention (mdl), upward (at the chiral center) in Daylight's (daylight).mdl
explicitHShow (true) or hide (false) explicit hydrogens.true
ezVisibleShow (true) or hide (false) E/Z labels.false
grinvShow (true) or hide (false) graph invariantsfalse
implicitHHow to display H labels.
  • off
  • hetero - on heteroatoms
  • heteroterm - on hetero or terminal atoms
  • all - all atoms
false
ligandErrorVisibleShow (true) or not (false) ligand error by coloring to red.false
lonePairsVisibleShow (true) or hide (false) lone pairsfalse
peptideDisplayTypeShow peptide sequences with one letter or three letter abbreviations.
Valid values are "1-letter" and "3-letter"
3-letter
rgroupsVisibleShow (true) or hide (false) R-group definitionstrue
selection0
selection1
selection2
...
Comma-separated list of atom numbers (0, ..., n-1).
Selected atoms are highlighted.
In a simple one-molecule viewer, selection0 must be used. In a molecule table, selectionn corresponds to molecule cell n.
 
showSetsShow the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63).heteroterm
sketchAnyBondDisplay type of the Any bond in the sketcher:
  • auto - displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).
  • dashed - displayed as dashed line
  • solid - displayed as solid line
auto
valenceErrorVisibleInViewShow (true) or hide (false) valence errorstrue
viewAnyBondDisplay type of the Any bond in the viewer:
  • auto - displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).
  • dashed - displayed as dashed line
  • solid - displayed as solid line
auto
zeroBasedAtomIndexingStarts the atom indexing from zero instead of one:
  • true - atom indexes are started from zero
  • false - atom indexes are started from one
false
viewAtomMarkEnabledEnables (true) or disables (false) atom highlight and atom mark in View.true
viewCarbonVisibilityDisplay the label of carbon atoms in structures.
  • on - Always show the atom labels of carbon atoms.
  • off - Never show the atom labels of carbon atoms.
  • inChain - Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.
inChain
viewLigandOrderVisibilityDisplay the ligand order of R-group atoms in structures.
  • on - Always show the ligand order of R-group atoms.
  • off - Never show the ligand order of R-group atoms.
  • showOnlyWithDefinition - Show the ligand order of R-group atoms only on R-groups with definition.
off