Here’s a file you can download.

The file can come with descriptions, etc.

You can also embed images:

This program uses a pdb and topology file to calculate 3J couplings and NOE’s.  This calculation is approximate because only a single frame is used and with the 1/r^6 approximation for the NOE calculation.  There are additional improvements to be added soon such as the inclusion of STD NOE’s and output of 2d NOESY spectra (simulated).  These improvements are done, but not yet included.

How to obtain the program

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

SingleFrameNMR
SingleFrameNMR.tar_.gz
Version: 1.0

941.4 KiB
257 Downloads
Details

This software uses a pdb and topology file to calculate noe's and 3J couplings. Documentation is included. The calculation is approximate due to the use only of a single frame and not a trajectory. It will eventually be used to provide the user these nmr observables in the download of a structure at glycam. The package can be downloaded now.

Languages:	English
Author:	Gordon Chalmers
Platforms:	Linux
Requirements:	GLYLIB
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation is included.
Other Contributors:	Rob Woods
Date:	June 22, 2017

The program is also available for download here:

Software Downloads

Associated Publication

Direct NOE Simulation from Long MD Trajectories.  G. Chalmers, J.N. Glushka, B.L. Foley, R.J. Woods, J.H. Prestegard.  Journal of Magnetic Resonance.  2016.  http://dx.doi.org/10.1016/j.jmr.2016.01.006

Installation

Installation instructions are included in the download referenced at the top of this page.

Usage

Use instructions are included in the download referenced at the top of this page.

This program uses Amber trajectories to calculate average 3J couplings.  It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories.  There are several types of options that the program can use.

How to obtain the program

This program uses Amber trajectories to calculate average 3J couplings.  It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories.  There are several types of options that the program can use.

How to obtain the program

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

3J_coupling_distribution
3J_coupling_distribution.tar_.gz
Version: 1.1

1.3 MiB
429 Downloads
Details

This program uses Amber trajectories to calculate average 3J couplings. It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories. There are several types of options that the program can use. Program error corrected.

Languages:	English
Author:	Gordon Chalmers
Platforms:	Linux
Requirements:	GLYLIB
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation is included
Other Contributors:	Rob Woods, Lachele Foley
Date:	April 18, 2016

The program is also available for download here:

Software Downloads

Associated Publication

None

Installation

Installation instructions are included in the download referenced at the top of this page.

Usage

Use instructions are included in the download referenced at the top of this page.

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

This program uses Amber trajectories to calculate average 3J couplings.  It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories.  There are several types of options that the program can use.

This is a package that calculates spin-spin and spin-lattice relaxation rates from trajectories.  This program can be used for well-sampled trajectories such as small molecules, and also with large molecules such as proteins and in not so well sampled trajectories.  In the latter case the ‘sphere’ approximation is used in which an artificial tumbling is added to a frame aligned trajectory.  This sphere approximation substantially improves the sampling.  The software has been successfully used with work on the skp1 protein.

How to obtain the program

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

particular_relaxation_rate
particular_relaxation_rate.tar_.gz
Version: 1.0

107.9 MiB
238 Downloads
Details

This is a package that calculations spin-spin and spin-lattice relaxation rates. The program can be used for well sampled trajectories, as found in small molecules, and also for proteins. In the latter case, the non-well sampled trajectory is handled by a 'sphere approximation,' in which artificial tumbling is added to the frame aligned trajectory. This substantially improves the sampling. As always, I am sure there will be some minor revisions.

Languages:	English
Author:	Gordon Chalmers
Platforms:	Linux
Requirements:	GLYLIB
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation and examples are included.
Associated Publications:	Glycosylation modulates the F-box combining site in Dictyostelium Skp1, M. Osman Sheikh, David Thieker, Christopher M. Schafer, Gordon Chalmers, Xianzhong Xu, Robert Woods, John N. Glushka, Brad Bendiak, James H. Prestegard, and Christopher M. West, to be submitted.
Date:	April 18, 2017

The program is also available for download here:

Software Downloads

Associated Publication

Glycosylation associated with O2-sensing modulates the F-box combining site of Dictyostelium Skp1, JBC,

Installation

Installation instructions are included in the download referenced at the top of this page.

Usage

Use instructions are included in the download referenced at the top of this page.

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

This program uses Amber trajectories to calculate average 3J couplings.  It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories.  There are several types of options that the program can use.

This software uses rdc, chemical shift, and noe measurements. It also uses chemical shift and noe predictions. The program can use any number of media, e.g. peg, phage. The program uses a genetic algorithm to find the matching of measurements to residues. There is additional documentation in the Assign_SLP_1.12.

There are two related programs, MD2NOE_Protein and Assign_SLP_MD, which are not yet on glycam, which can also be found at the Prestegard Software site.

How to obtain the program

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

ASSIGN SLP Redirect
ASSIGN_SLP_redirect.docx

11.8 KiB
443 Downloads
Details

This is a Matlab package that uses NMR experimental measurements and calculations in a genetic algorithm to sparsely label proteins. RDC's, noe's, and chemical shifts are used. The
software was developed in the Prestegard lab, and is available at that group's software website. I work in the Prestegard and Woods group at CCRC UGA and contribute software to glycam. Because we don't want multiple versions at different sites, only the link is given to the website. The package can be downloaded from

http://tesla.ccrc.uga.edu/software/ASSIGN_SLP/Assign_SLP_1.12.zip

Feel free to download from here and there. If you hit download here you won't get anything, except it will show how many downloads there are - so please hit the download here so we can keep track of how much usage there is, which is important.

Author:	Qi Gao, Gordon Chalmers, Kelly Moreman, James Prestegard
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation is included.
Associated Publications:	Submitted to the Journal of Biomolecular NMR. "NMR Assignments of Sparsely Labeled Proteins Using a Genetic Algorithm," Qi Gao^*; Gordon R Chalmers^*; Kelley W Moremen; James H Prestegard.
Date:	January 24, 2017

The download gives a file showing where to find the program.  It, and the documentation, can be found at the Prestegard software site, http://tesla.ccrc.uga.edu/software/.  We did not want multiple versions on 2 sites, and the work was primarily done with Professor Prestegard.

The program is also available for download here:

Software Downloads

Associated Publication

Pederson, K., Chalmers, G. R., Gao, Q., Elnatan, D., Ramelot, T. A., Ma, L. C., Montelione, G. T., Kennedy, M. A., Agard, D. A., and Prestegard, J. H. (2017) NMR characterization of HtpG, the E-coli Hsp90, using sparse labeling with C-13-methyl alanine, Journal of Biomolecular Nmr 68, 225-236.

Installation

Installation instructions are included in the download referenced at the top of this page.

Usage

Use instructions are included in the download referenced at the top of this page.

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

This program uses Amber trajectories to calculate average 3J couplings.  It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories.  There are several types of options that the program can use.

Click on an image to watch a short video of the system. Or, download a copy by right-clicking the image and choosing “Save Link As…”

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 433 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 453 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 537 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 522 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