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Gorgon

Thursday PM Practical

Gorgon is an interactive molecular modeling system specifically geared towards near-atomic resolution density maps of macromolecular assemblies. It is being developed as a collaboration between Washington University in St. Louis (Tao Ju) and Baylor College of Medicine (Matthew Baker).

Gorgon currently provides the following feature categories:

Visualization: A comprehensive visualization framework for volumetric data (iso-contours, cross-sections and solid rendering), geometric skeletons, secondary structure elements and atomic models (PDB).
Geometric operations: Many geometric operations such as skeletonization (binary / grayscale and interactive), smoothing, resampling, cropping, etc. are provided.
Secondary structure identification: SSEHunter is now integrated into Gorgon, which lets you to find the locations of Alpha Helices and Beta Sheets given a low-resolution density map.
Protein backbone tracing: The C-alpha backbone of a protein can be easily traced manually or semi-automatically using the many supporting elements offered by Gorgon.

For the workshop, we will use Gorgon to identify secondary structure elements identification, fit atomic models and trace the backbone of protein in a near-atomic resolution cryo-EM density map. Additionally, we will use Pathwalker, a new modeling tool available in EMAN2, to automatically trace a protein backbone.

Sample data can be downloaded here: WorkshopData.zip

Gorgon can be downloaded at: http://gorgon.wustl.edu/

A new version of e2pathwalker.py can be found here

For those of you using a laptop, please also install the LKH solver used in our pathwalker demo. http://www.akira.ruc.dk/~keld/research/LKH/

The Gorgon publication with videos can be found at http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WM5-523M8D1-5&_user=10&_coverDate=02%2F04%2F2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_searchStrId=1675218671&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a054a311592fda2c79f5c043830e6b75&searchtype=a

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-  ⇤ ← Revision 7 as of 2011-03-11 22:49:53 → 
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-The Gorgon publication with videos can be found at http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WM5-523M8D1-5&_user=10&_coverDate=02%2F04%2F2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_searchStrId=1675218671&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a054a311592fda2c79f5c043830e6b75&searchtype=a
+The Gorgon publication with videos can be found at [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WM5-523M8D1-5&_user=10&_coverDate=02/04/2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_searchStrId=1675218671&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a054a311592fda2c79f5c043830e6b75&searchtype=a|http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WM5-523M8D1-5&_user=10&_coverDate=02%2F04%2F2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_searchStrId=1675218671&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a054a311592fda2c79f5c043830e6b75&searchtype=a]]