MarvinView Structure Display Parameters

    Parameter Meaning Default
    absLabelVisible Show (true) or hide (false) "Absolute" label false
    aminoAcidBondColoringEnabled Enable (true) or disable (false) peptide bridge coloring true
    atomFont Atom symbol/label font: Serif, SansSerif or Monospaced SansSerif
    atomMappingVisible Show (true) or hide (false) atom mapping true
    atomPropertiesVisible Show (true) or hide (false) atom properties true
    atomNumbersVisible Deprecated N/A
    atomNumberingType Sets the type of atom numbering to Off(0), Atom numbers (1) or IUPAC numbering (2) 0
    valencePropertyVisible Show (true) or hide (false) valence properties true
    atomsize Atom symbol font size in C-C bond length units: atomsize 1.54 Å = atomsize scale points, where scale is the current magnification. 0.4
    atomSymbolsVisible Show (true) or hide (false) atom symbols in 3D view true
    bondLengthVisible Show (true) or hide (false) bond length labels false
    bondSpacing Double bond spacing in C-C bond length units: spacing 1.54 Å = spacing scale pixels, where scale is the current magnification. 0.18
    chargeWithCircle Charge label (plus or minus sign) is displayed circled(true) or normal(false) false
    chiralitySupport When 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
    circledChargeFont Circled charge labels font: any of the fonts installed on the machine. Deprecated, will be removed by January 1st, 2016. SansSerif
    circledChargeSize Deprecated. N/A
    colorScheme Color scheme.
    mono - monochrome
    cpk - Corey-Pauling-Kultun
    shapely - shapely (residue types)
    group - residue sequence numbers
    cpk
    downWedge Wedge bond display convention. Down wedge points downward in MDL's convention (mdl), upward (at the chiral center) in Daylight's (daylight). mdl
    explicitH Show (true) or hide (false) explicit hydrogens. true
    ezVisible Show (true) or hide (false) E/Z labels. false
    grinv Show (true) or hide (false) graph invariants false
    implicitH How to display H labels.
    off
    hetero - on heteroatoms
    heteroterm - on hetero or terminal atoms
    all - all atoms
    false
    ligandErrorVisible Show (true) or not (false) ligand error by coloring to red. false
    lonePairsVisible Show (true) or hide (false) lone pairs false
    peptideDisplayType Show peptide sequences with one letter or three-letter abbreviations. Valid values are "1-letter" and "3-letter" 3-letter
    rgroupsVisible Show (true) or hide (false) R-group definitions true
    selection0selection1selection2... 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, selection n corresponds to molecule cell n . N/A
    showSets Show the specified atom sets only. A comma-separated list of set sequence numbers (0, ..., 63). heteroterm
    sketchAnyBond Display type of the Any bond in the sketcher:
    auto - displayed as a 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 a dashed line
    solid - displayed as a solid line
    auto
    valenceErrorVisibleInView Show (true) or hide (false) valence errors true
    viewAnyBond Display type of the Any bond in the viewer:
    auto - displayed as a 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 a dashed line
    solid - displayed as a solid line
    auto
    zeroBasedAtomIndexing Starts the atom indexing from zero instead of one:
    true - atom indexes are started from zero
    false - atom indexes are started from one
    false
    viewAtomMarkEnabled Enables (true) or disables (false) atom highlight and atom mark in View. true
    viewCarbonVisibility Display 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 implicit Hydrogens.
    inChain
    viewLigandOrderVisibility Display 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 a definition.
    off