Tag Archives: Software

Which applications are available for visualizing downloaded files?

Once the build of the carbohydrate molecule is complete, it can be downloaded and visualized. Visual molecular dynamics (VMD) is one program that can be used to visualize these files. VMD displays molecular surfaces with fast surface calculation and display. The high performance algorithms allow even complex surfaces to be displayed. To download this program click […]

Visualizing PDB Files Containing Glycans

Carbohydrates in the PDB and VMD For reasons that are mostly historical, carbohydrates are currently not treated well in non-specialist databases such as the PDB or in visualization software such as VMD.  Efforts are underway to improve the situation.  In the meantime, this exercise will explain some of the problems, and offer some ways to […]

BFMP Tutorial 2

Determining the ring conformation of Iduronic acid from a PDB file using BFMP. If needed, please click here for instructions on downloading and installing the BFMP program. The program requires two input files: a text file in PDB format and a configuration file. Click here to download BFMP-Tutorial2.tar.gz, the input and output files for this tutorial Using vi or […]

BFMP Tutorial 1

Determining the ring conformation of A-L-Idopyranose during the course of a 10ns MD simulation using BFMP. If needed, please click here for instructions on downloading and installing the BFMP program. The program requires three input files: an AMBER format topology file, AMBER format trajectory file and a configuration file. Click here to download BFMP-Tutorial1.tar.gz, the Input AMBER format files and output […]