Command: snfg

Usage:
snfg [ show ] [ structures  model-spec ] [ size  angstroms ] [ atoms  true | false ]

Usage:
snfg hide [ structures  model-spec ]

The snfg command depicts carbohydrate residues using the 3D-SNFG (Symbol Nomenclature for Glycans), a community standard for representing different sugars with geometric shapes and colors:

Symbol Nomenclature for Graphical Representations of Glycans. Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, Prestegard JJ, Schnaar RL, Freeze HH, Marth JD, Bertozzi CR, Etzler ME, Frank M, Vliegenthart JF, Lütteke T, Perez S, Bolton E, Rudd P, Paulson J, Kanehisa M, Toukach P, Aoki-Kinoshita KF, Dell A, Narimatsu H, York W, Taniguchi N, Kornfeld S. Glycobiology. 2015 Dec;25(12):1323-4.
3D implementation of the symbol nomenclature for graphical representation of glycans. Thieker DF, Hadden JA, Schulten K, Woods RJ. Glycobiology. 2016 Aug;26(8):786-7.

Shape	Sugar Class	Examples
Sphere	Hexoses	Glucose (blue), Mannose (green), Galactose (yellow)
Cube	N-acetylhexosamines	GlcNAc (blue), GalNAc (yellow)
Diamond	Hexuronic acids, Sialic acids	GlcA (blue), Neu5Ac (purple)
Cone	Deoxyhexoses	Fucose (red), Rhamnose (green)
Star	Pentoses	Xylose (orange), Arabinose (green)
Rectangle	Di-deoxyhexoses	Olivose, Tyvelose
Hexagon	Heptoses	Kdo (yellow), MurNAc (purple)
Pentagon	Ketoses	Fructose (green), Apiose (blue)

Colors indicate stereochemistry within each shape class: blue (Glc-type), green (Man-type), yellow (Gal-type), orange (Gul-type), pink (Alt-type), purple (All-type), light blue (Tal-type), brown (Ido-type), red (Fuc/Sia). Common carbohydrate residues are identified by their PDB residue names (NAG, MAN, FUC, GAL, etc.) as per the wwPDB Chemical Component Dictionary.

See also: nucleotides, cartoon, aniso, shape, BILD format, the NCBI SNFG page

The snfg show or snfg command displays 3D-SNFG representations of glycans in the specified structures (atomic models), or all atomic models if none are specified. The 3D-SNFG shapes are placed at the centroid of the sugar ring, or if no ring is detected, at the residue center of mass.

• The size option sets symbol diameter (default 4.0 Å, the approximate diameter of a monosaccharide ring).
• The atoms option controls whether to keep the current display states of the glycan atoms (default true, those which are shown remain shown and those which are hidden remain hidden). Specifying atoms false hides the glycan atoms when the SNFG representations are shown. Either way, however, the glycan atoms can be subsequently hidden or shown regardless of whether the 3D-SNFG symbols are present.

The command snfg hide removes 3D-SNFG representations from the specified structures (atomic models), or all atomic models if none are specified.

Example commands:

snfg
snfg atoms false
snfg hide
snfg structures #1
snfg size 6