Description

The following tables define the residue names that are recognized within the 3D-SNFG program, and are separated based on the source: PDB, GLYCAM, and CHARMM*. Some monosaccharide residues that are defined by the SNFG are uncommon, and not currently used by any of these sources. While the 3D-SNFG program is capable of drawing the appropriate shapes/colors for these uncommon residues, they will not be recognized unless the user defines the residue names within the code manually.

Quickly navigate between the three nomenclatures via the table of contents (above). The columns may be sorted by clicking on the respective header. If searching for a specific residue name, use the ‘Find’ function within your web browser.

*Note: Some CHARMM carbohydrate residue names are longer than the four-character field allocated in standard PDBs and XPLOR-format PSF files (used in NAMD). In that case, residue recognition will depend on what four-character residue name is substituted in these files for the full CHARMM residue name. If a file was produced with PSFGEN, the user likely selected an alternate residue name that fit within the four-character constraint, and will need to add the new residue name to the appropriate CHARMM list within the script to ensure recognition. However, if a file was produced with CHARMM-GUI, the residue name may simply have been truncated to four characters, causing recognition conflicts. For example, in the case of GlcNAc, CHARMM-GUI truncates BGLCNA to BGLC. As BGLC is the standard CHARMM residue name for glucose, 3D-SNFG will recognize the residue as glucose, even though it is structurally an N-acetyl-glycosamine.

PDB

GLYCAM

CHARMM