Glycobiology

RayMol integrates dedicated glycobiology tools directly into its molecular model and Metal rendering pipeline. Recognized carbohydrate residues can be displayed as three-dimensional Symbol Nomenclature for Glycans (SNFG) shapes or colored using the standard SNFG palette, while the underlying atomic coordinates remain fully interactive and inspectable.

SNFG conventions & residue catalogue

RayMol adheres to the Symbol Nomenclature for Glycans (SNFG) standard established by the glycomics community and NCBI. Carbohydrate residues are represented by standardized geometric shapes and colors based on their monosaccharide family.

The built-in catalogue covers the most common mammalian monosaccharides and their chemical-component PDB identifiers:

PDB Code	Monosaccharide	SNFG Symbol	3D Shape	Color	Hex Code
NAG, NDG	N-acetylglucosamine	GlcNAc	Cube	Blue	#0072BC
A2G, NGA	N-acetylgalactosamine	GalNAc	Cube	Yellow	#FFD400
BM3	N-acetylmannosamine	ManNAc	Cube	Green	#00A651
MAN, BMA	Mannose	Man	Sphere	Green	#00A651
GAL, GLA	Galactose	Gal	Sphere	Yellow	#FFD400
GLC, BGC	Glucose	Glc	Sphere	Blue	#0072BC
FUC, FUL	Fucose	Fuc	Cone	Red	#ED1C24
SIA, SLB	N-acetylneuraminic acid	Neu5Ac	Diamond	Purple	#A54399
NGC	N-glycolylneuraminic acid	Neu5Gc	Diamond	Light Blue	#8FCCE9

Residue codes not in this table are left untouched; a catalogued residue whose ring atoms are incomplete gets no 3D symbol.

Rendering SNFG cartoons

When an SNFG cartoon is generated, RayMol computes the centroid and ring normal of each complete sugar ring, renders the corresponding 3D geometric symbol, and traces covalent glycosidic bonds between residues as cylindrical linkers. Linkers reflect true covalent connectivity, not arbitrary spatial proximity.

SNFG glycan cartoon of a sialylated IgG Fc (PDB 4BYH).

From the interface

In the Objects panel:

• Open the S menu on an object row and choose Glycan cartoon to generate the 3D symbols.
• Open the H menu on an object row and choose Glycan cartoon to remove its 3D symbols and show those sugar residues as sticks.
• Open the C menu on an object row and choose SNFG glycan palette to color the underlying atomic model according to SNFG standards without generating 3D cartoon shapes.

From the command line

Run glycocartoon and glycocolor directly in the command entry bar:

fetch 4byh, async=0
glycocolor 4byh
glycocartoon 4byh

To customize cartoon dimensions or linkers, supply the optional arguments:

glycocartoon [selection [, size [, draw_linkers [, state]]]]

• selection (default "all"): The target atom selection.
• size (default 2.5): The geometric scale of the generated 3D symbols in angstroms.
• draw_linkers (default 1): Set to 1 to render connecting cylinders along glycosidic bonds, or 0 to render only the monosaccharide symbols.
• state (default 1): Coordinate state index for multi-state objects.

Hiding cartoons

To remove one cartoon, pass the same selection text you gave glycocartoon (e.g. glycocartoon_hide 4byh after glycocartoon 4byh). If unsure, use glycocartoon_hide_all.

glycocartoon_hide 4byh

To remove all generated glycan cartoon objects across the entire session and show those sugar residues as sticks:

glycocartoon_hide_all

Interactive picking

Clicking a sugar symbol acts like clicking that residue’s atoms, so it works with the current selection or measurement mode.

Inspecting glycan topology & geometry

Complex N- and O-linked glycans form branched tree structures rooted at protein attachment sites (such as asparagine for N-glycosylation or serine/threonine for O-glycosylation).

The Glycan Topology panel

To inspect the glycan forest interactively:

The Glycan Topology sheet for the IgG Fc N-glycans of 4BYH.

1. Locate the OBJECTS section header in the Objects panel.
2. Click the indented-list icon (Glycan topology) at the right of the OBJECTS header.
3. The Glycan Topology sheet opens, displaying each glycan tree, rooted at the sugar covalently bonded to a non-sugar residue (for example the Asn of an N-glycan) when there is one. The header shows the residue and component counts.

Each node in the topology tree details:

• Residue: SNFG symbol, residue name, number and chain.
• Ring shape: a coarse puckering class (chair-like, boat/skew-like, envelope/half-chair-like, nearly planar).
• Linkage: the bond atoms (e.g. C1-O4).

Numeric Cremer–Pople Q/θ/φ and glycosidic φ/ψ (and ω for 1→6 linkages) are available from the glyco_tree command. Clicking any node in the topology list highlights and centers that residue in the 3D viewport.

Topology commands

The same structural analysis can be invoked from the command bar or Python scripts:

glyco_tree [selection [, state]]
glyco_remediate [selection [, state]]

• glyco_tree: Constructs the covalent glycan tree hierarchy, measures ring puckering parameters, calculates glycosidic torsion angles, and prints the result as JSON (residues, Cremer–Pople Q/θ/φ, linkage φ/ψ/ω).
• glyco_remediate: Reports, for each residue in the selection, whether its residue code is in RayMol’s SNFG catalogue. For unknown codes it says whether the atom names suggest an aldose-like or sialic-acid-like ring. Nothing is changed; output is JSON.

Advisory geometry

Puckering classifications and torsion angle assessments are advisory structural metrics. They do not alter coordinates or rewrite PDB residue identities, and should be interpreted in conjunction with experimental electron density or cryo-EM map evidence.