Structure Display Parameters

Parameter

Meaning

Default

absLabelVisible

Show (true) or hide (false) "Absolute" label

false

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

Can be given in pt ie.:msketch_param(\"atomsize\", \"16 pt\");

0.35714285714285715

(10pt)

atomSymbolsVisible

Show (true) or hide (false) atom symbols

true

automaticFogEnabled

Deprecated.

ballRadius

Ball radius for ballstick rendering mode, in units of the covalent radius.

0.5

boldBondWidth

Width of bold bond in pt.

6

bondLength

Lenght of bond in pt.

28

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

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 a chiral flag is set for the molecule or the atom's enhanced stereo type is absolute

  • all - always

  • allPossible - show all chiral centers and highlight possible but undefined centers too

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-Koltun

  • 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 (daylight).

mdl

explicitH

Show (true) or hide (false) explicit hydrogens

true

ezVisible

Show (true) or hide (false) E/Z labels

false

fogFactor

Set the custom fog factor in a range from 0 to 100. The value 100 is for the strongest fog and 0 for the weakest (no) fog.

66

grinvVisible

Show (true) or hide (false) graph invariants (canonical labels)

false

implicitH

How to display H labels.

  • off

  • hetero - on heteroatoms

  • heteroterm - on hetero or terminal atoms

  • all - all atoms

heteroterm

ligandErrorVisible

Show (true) or not (false) ligand error by coloring to red

true

lonePairsVisible

Show (true) or hide (false) lone pairs

false

lonePairsAutoCalc

Switch on (true) or off (false) automatic calculation of lone pairs. The lonePairsVisible parameter should be set to true to display the result of the automatic calculation.

false

maxscale

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

peptideDisplayType

Show peptide sequences with one letter or three-letter abbreviations.
Valid values are "1-letter" and "3-letter"

3-letter

reactionErrorVisible

Deprecated.

false

rendering

Rendering style.

  • wireframe - wireframe

  • sticks - 3D sticks

  • ballstick - ball & stick

  • spacefill - balls

wireframe

rgroupsVisible

Show (true) or hide (false) R-group definitions.

true

scale

Magnification. A 1.54 Å long C-C bond is magnified to scale pixels.

28

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

stickdst

Stick distance of atoms in C-C bond length units.

0.3

showSets

Show the specified atom sets only. A comma-separated list of set sequence numbers (0, ..., 63).

sketchCarbonVisibility

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

sketchLigandOrderVisibility

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

stickThickness

3D stick diameter for "sticks" and ballstick rendering modes, in Angstroms.

0.1

valenceErrorVisible

Highlight (by underlining) the labels of those atoms with valence errors. This option can also be set on the Edit/Preferences/MarvinSketch panel.

  • true - display errors

  • false - do not display 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

wireThickness

Line thickness for wireframe and wireknobs rendering modes, in Angstroms.

0.064