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Antibody-Receptor

PDB ID: 3SGJ

Erythropoitin Glycoform

PDB ID: 1BUY – Glycans added with Glycoprotein Builder | Tutorial

Glycans¹

The .pdb file used to generate each image may be downloaded by clicking on the respective titles.

Branched Glycan

Notice that the glycan appears linear without the label for the reducing terminus (far right).

High Mannose

Heparan Sulfate Attachment

Heparan Sulfate Fragment

Xyloglucan

Complex N-Glycan (CFG Array #484)

Glycan-Protein Complexes

Salmonella Antibody SE155-4

(PDB ID: 1MFB)

 Glycoproteins

Erythropoietin Glycoform¹

PDB ID: 1BUY – Glycans added with Glycoprotein Builder | Tutorial

Antibody-Receptor

PDB ID: 3SGJ

Example Shapes

¹The glycans were built with the GLYCAM Webtool

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

Description

The Symbol Nomenclature For Glycans (SNFG) facilitates the efficient communication of carbohydrate structures, and has become widely accepted by the glycobiology community. The system is fully described in the NCBI text Essentials of Glycobiology.

Carbohydrates currently lack a simplistic, standardized representation for 3D structure, and are thus predominantly visualized with atoms displayed. Discerning the glycan sequence from these atomistic views is challenging, even for short  for oligosaccharide chains. The following software generates 3D shapes that match the SNFG format (both color and shape), and positions them on the geometric center of carbohydrate rings that are identified within a PDB file. This representation generates a cartoon-like representation for glycans within the Visual Molecular Dynamics (VMD) program. Automated recognition of monosaccharides relies upon commonly employed residue¹ and atom names.²

¹The current list of recognizable residue names includes common names from the PDB, as well those from the GLYCAM and CHARMM forcefields. Unknown residues are depicted as white, flat hexagons
²The ring atoms must be C1, C2, C3, C4, C5, and O5, unless the monosaccharide is a sialic acid, in which case they should be named C2, C3, C4, C5, C6, and O6

Installation

Note: VMD installation is discussed in the documentation of Ancilliary Software.

Step 1) Download

Two options are provided that differ by the VMD ‘default’ settings. Option 1 only includes the 3D-SNFG representations, and maintains the original settings for VMD. Option 2 contains the 3D-SNFG script, as well as a few aesthetic changes that are loaded at startup (i.e. white background, automatic representation of proteins with NewCartoon, etc.).  The 3D-SNFG representations are identical in both cases.

Details: A vmdrc file allows you to customize the default settings of VMD. Option 2 initializes multiple representations in order to display the protein backbone as a cartoon, side chains as sticks, and all other atoms as licorice. The background has been changed to white, labels to black,, and display set to an orthographic view. Other options can be useful, such as changing the size and position of windows.

Option 1	Option 2
Linux & Macintosh: Download the following .vmdrc file 3D-SNFG Option 1 (Linux/Macintosh) 3D-SNFG_v1_default-vmdrc_Linux-Mac.zip Version: 1 15.3 KiB 434 Downloads Details The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures. Author: David F. Thieker Category: Publication Software License: CC Attribution-NonCommercial-ShareAlike Documentation: Full documentation is available at http://glycam.org/3d-snfg Associated Publications: Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) Related Publications: Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 Other Contributors: Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods Date: June 21, 2016	Linux & Macintosh: Download the following .vmdrc file 3D-SNFG Option 2 (Linux/Macintosh) 3D-SNFG_v1_mod-vmdrc_Linux-Mac.zip 15.4 KiB 454 Downloads Details The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures. Author: David F. Thieker Category: Publication Software License: CC Attribution-NonCommercial-ShareAlike Documentation: Full documentation is available at http://glycam.org/3d-snfg Associated Publications: Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) Related Publications: Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 Other Contributors: Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods Date: June 21, 2016
Windows: Download the following vmd.rc file 3D-SNFG Option 1 (Windows) 3D-SNFG_v1_default-vmdrc_Windows.zip Version: 1 15.3 KiB 538 Downloads Details The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures. Author: David F. Thieker Category: Publication Software License: Apache 2.0 Documentation: Full documentation is available at http://glycam.org/3d-snfg Associated Publications: Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) Related Publications: Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 Other Contributors: Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods Date: July 11, 2016	Windows: Download the following vmd.rc file 3D-SNFG Option 2 (Windows) 3D-SNFG_v1_mod-vmdrc_Windows.zip Version: 1 15.4 KiB 523 Downloads Details The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures. Author: David F. Thieker Category: Publication Software License: CC Attribution-NonCommercial-ShareAlike Documentation: Full documentation is available at http://glycam.org/3d-snfg Associated Publications: Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) Related Publications: Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 Other Contributors: Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods Date: June 21, 2016

Experienced VMD Users: You can source the 3D-SNFG script within your personal vmdrc file. The provided vmdrc files consist of two parts, the initialization of VMD and the 3D-SNFG tcl script. Rename the provided vmdrc file 3D-SNFG_v1.tcl, and remove all of the lines above ‘# Load the 3D-SNFG script’. Now source this script within your personal vmdrc.

Step 2) Install

Move the file to either your home directory, or the location where the VMD software is installed, and unzip the file.

Note that the unzipped file is named .vmdrc on Macintosh and Linux systems. A period that precedes a filename designates the file as “hidden”. Although the unzipped contents may appear empty, the file will be recognized by VMD.

Step 3) Visualize

Load a file containing a glycan into VMD (i.e. PDB ID: 3SGJ). On your keyboard, use the following shortcut keys:

• ‘i’ – apply the SNFG-Icons representation
• ‘g’ – apply the 3D-SNFG representation
• ‘b’ – apply the 3D-SNFG representation and label the reducing terminus
• ‘d’ – delete the drawn objects

FAQ

• Are structures available to test my setup?
• Does the code discriminate between D- and L- residues?
• How were the sizes of the 3D-SNFG shapes selected?
• How are modifications represented (i.e. sulfate and phosphate)?
• How do I draw 3D-SNFG objects on a molecule other than the most recently loaded file?
• How do I change the shape of an unrecognized residue (flat, white hexagon)?
• What does “ERROR) No molecules loaded” mean?
• Why are some of the shapes missing?
• Why are all of the shapes missing?
• How are the shapes built?

Advanced Usage

• Introduce new residue names
• Change the material of the 3D-SNFG shapes
• Color monosaccharide atoms according to the SNFG
• Combine 3D-SNFG with a Trajectory Smoothing Window

Gallery

• Images

• Videos

Questions/Comments

If you have any issues that are not covered in the FAQ, or would like to provide suggestions for the representations, please contact us.

Citation

Thieker, D. F., Hadden, J. A., Schulten, K., & Woods, R. J. (2016). 3D implementation of the Symbol Nomenclature for Graphical Representation of Glycans. Glycobiology, 26(8), 786-787. DOI:10.1093/glycob/cww076)

Associated Publications

SNFG Update | Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., … & Prestegard, J. J. (2015). “Symbol Nomenclature for Graphical Representations of Glycans.” Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091

VMD | Humphrey, W., Dalke, A. & Schulten, K. (1996). “VMD – Visual Molecular Dynamics”, J. Molec. Graphics, 14 (1), 33-38. DOI: 10.1016/0263-7855(96)00018-5