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 command snfg show shows 3D-SNFG representations of glycans in the specified structures (atomic models), or all if none are specified. 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 representations are present.
The command snfg hide removes 3D-SNFG representations from the specified structures (atomic models), or all if none are specified.
Example commands:
snfg– show SNFG symbols for glycans in all atomic structures
snfg structures #1– show SNFG symbols for glycans in model #1
snfg size 6– show larger (6-Å) SNFG symbols
snfg atoms false– show SNFG symbols only, hiding the sugar atoms
snfg hide– remove all SNFG symbols
Sugar residues are identified by their PDB residue names (e.g., NAG, MAN, FUC, GAL). The command recognizes common carbohydrate residue codes from the wwPDB Chemical Component Dictionary.
SNFG symbols are placed at the centroid of the sugar ring (pyranose or furanose). If no ring is detected, the symbol is placed at the residue center of mass.