VMD
A complex between a model of Mbp1 and a segment of DNA
The model was visualized and positioned in VMD - nucleotides were displayed as "licorice" sticks and the protein was covered by its solvent-accessible surface, calculated with a probe radius of 1.4 Å. Coloring is according to position. The scene was rendered with the tachyon raytracer using ambient occlusion lighting and 8-fold antialiasing.
The model was visualized and positioned in VMD - nucleotides were displayed as "licorice" sticks and the protein was covered by its solvent-accessible surface, calculated with a probe radius of 1.4 Å. Coloring is according to position. The scene was rendered with the tachyon raytracer using ambient occlusion lighting and 8-fold antialiasing.
VMD (viual molecular dynamics) is a powerful, well engineered, molecular graphics package. It is one of a number of freely available tools to visualize and manipulate three-dimensional molecular datasets, but it stands out due to its rich features, the versatility of its use and the ease with which common tasks can be accomplished and the fact that it is being actively developed and maintained.
Contents
Installing VMD
- Access the VMD homepage and navigate to the download section.
- Follow the link to the newest version (1.8.6 as of this writing) and review the features.
- Access the Download page and click on the link appropriate for your platform. Follow the instructions to install VMD.
Basic molecular models
- Download the 1UBQ.pdb file from the PDB
- Start VMD on your computer
- Access the VMD tutorial, part 1 and go through the steps described there.
