Difference between revisions of "VMD"
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==VMD tutorials== | ==VMD tutorials== | ||
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| + | The '''VMD''' site has a [http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials tutorial section] with many excellent contributions. | ||
| − | * [[Stereo | + | The following links take you directly to the on-line tutorials at UIUC. |
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| + | *[http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node1.html '''Part 1 (Introduction)'''] | ||
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| + | *[http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html '''Part 2 (Working with a single molecule)'''] | ||
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| + | <!-- | ||
| + | * [[Stereo Vision]] | ||
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* [[VMD_tutorial_modelling|Mutation and Modeling]] | * [[VMD_tutorial_modelling|Mutation and Modeling]] | ||
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==Links and resources== | ==Links and resources== | ||
Revision as of 22:05, 13 September 2012
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 ramped according to position (i.e. an atom's distance from the complex's centre of mass). 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 ramped according to position (i.e. an atom's distance from the complex's centre of mass). 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.
Installing VMD
- Access the VMD homepage and navigate to the download section.
- Follow the link to the newest version (1.9.1 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.
VMD tutorials
The VMD site has a tutorial section with many excellent contributions.
The following links take you directly to the on-line tutorials at UIUC.
