MarvinView Structure Display Parameters

Parameter

Meaning

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

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

Circled 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

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, selectionn corresponds to molecule cell n.

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