From: Frieda R. <fri...@ma...> - 2008-11-10 18:45:35
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I am sending the efvet file under separate cover as it is 2.4 MB. (Apparently it is in xml format, whereas I had thought that efvet referred to the format) It is from a single protein chain of the pdb file 1LMB (efvet files also can contain information for multiple chains). Here is what the web site says about efvet: seqinfo and efvet files In this database system, two kinds of file, seqinfo file and efvet file, are used to keep all information for each entry. The seqinfo file describes biological functions of the molecule and chemical properties of each functional site on the molecular surface. The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are discribed together by the surface color in such a way that red to blue colors correspond negative to positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residue. The seqinfo file and efvet file are both written in XML and schema documents for them are available. I'm assuming you do not need the seqinfo file, which seems to contain information on the active site residues, but nothing regarding surface or potentials. It may be that the efvet file contains surface information but not potentials. That would be a bummer. But perhaps the authors would consider allowing access to more information. Note they also offer their own custom applet to display the surfaces and structures, but it has nowhere near Jmol's functionality. Here is the link to the schema for efvet: http://ef-site.hgc.jp/eF-site/schema/efvet30.xsd Thanks, Frieda On Nov 10, 2008, at 12:06 PM, Robert Hanson wrote: > Sounds very interesting. What's more, Jmol could display the data as > JVXL files possibly and compress the data immensely. > > Do you have some of these files, Frieda? > > On Mon, Nov 10, 2008 at 9:48 AM, Frieda Reichsman > <fri...@ma...> wrote: > Hi Bob, > > eF-site ( http://ef-site.hgc.jp/eF-site/ ) is a database for molecular > surfaces, coloring by electrostatic potential. Seems like the entire > contents of the pdb is available - a great resource. The MEP data can > be obtained in an "efvet" file, described here: > http://ef-site.hgc.jp/eF-site/about.html > > Could you take a look and consider including this file type in what > Jmol can read? (I tried to check whether Jmol can already read it - > efvet is not listed in the wiki, don't know if that is up to date, tho > - and the script documentation server appears to be down this > morning). > > Thanks, > Frieda > > > ---- > > Frieda Reichsman, PhD > Senior Research Scientist > The Concord Consortium > 25 Love Lane > Concord, MA 01742 > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |