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--- I believe the person wishes to view protein-protein interaction (PPI) networks using Jmol. I have been doing this for quite some time. Basically a PPI is just a bunch of proteins (nodes) and interactions (edges) between them. They can be interpreted as networks. However, to view them one must come up with a geometry. I have treated PPI networks as sort of big molecules and then optimized node coordinates for a simple "Energy" objective function (my background is quantum chemistry). Of course, some proteins (nodes) will have more interactions than others, and the ones that have the most, by far, are called hubs. I include a .gpr and script file (which reads in the .gpr) and colors some hubs red, while leaving the other nodes and edges grey. I have actually made a movie file from this by rotating by a degree, taking a snapshot, etc. The file uses Jmol to view the PPI network of E. coli determined from a particular experiment. Joe --- Dr. Joe Ivanic - Contractor, Foreign National Scientist Biotechnology HPC Software Applications Institute ATTN: MCMR-TT Building 363, Miller Drive Ft. Detrick, MD 21702-5012 Voice: (301) 619 1976 Fax: (301) 619 1983 -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Angel Herraez Sent: Friday, April 18, 2008 8:34 AM To: [email protected] Subject: Re: [Jmol-users] Hub and Non-Hub Hi lijo Could you please explain waht do you mean by "hub" and "hub protein"? Best if you provide an example file ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
