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.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).
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)
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. Common carbohydrate residues are identified by their PDB residue names (NAG, MAN, FUC, GAL, etc.) as per the wwPDB Chemical Component Dictionary. 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