From: Robert H. <ha...@st...> - 2008-11-12 13:50:30
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oooh -- now we're talking. Using a new algorithm I wrote last night, I'm getting 23:1 compression creating JVXL files from those efvet files. So the 20 Mb file comes down to 890K. And with gzip compression, that comes out 471K. So that's 43:1 compression. That should work for web-based delivery. An interesting aspect of this is that JVXL files now can be created in principal (i.e. with just a little coding) from any standard vertex/triangle "surface" file from any source. Very interesting! Thanks, Frieda! Bob On Tue, Nov 11, 2008 at 5:30 PM, Robert Hanson <ha...@st...> wrote: > Frieda, try http://www.stolaf.edu/people/hansonr/temp/Jmol-11.zip > > isosurface "xxxxx.efvet" > isosurface "xxxxx.efvet" 2 # > isosurface "xxxxx.efvet" 3 > isosurface "xxxxx.efvet" color "rwb" > isosurface "xxxxx.efvet" color "rwb" range 0.1 0.6 > > > 1 (default): electrostatic_potential > 2 hydrophobicity > 3 temperature_factor > 4 minimum_curvature > 5 maximum_curvature > > > > > > > > On Tue, Nov 11, 2008 at 2:05 PM, Frieda Reichsman <fri...@ma...>wrote: > >> An efvet file with protein and DNA chains is here: >> http://public.me.com/friedar22/Jmol >> Ignore the other file, it is irrelevant. >> >> On Nov 11, 2008, at 12:03 PM, Robert Hanson wrote: >> >> Jmol 11.7.11 will read these efvet files. No JVXL creation, though. The >> way it will work (for now) is that you indicate which data type you want >> with a number after the filename. >> >> Can you find any examples of efvet files that contain multiple surfaces? >> >> Bob >> >> >> >> >> On Mon, Nov 10, 2008 at 5:24 PM, Frieda Reichsman <fri...@ma...>wrote: >> >>> OK, I will see about contacting them. >>> >>> On Nov 10, 2008, at 5:28 PM, Robert Hanson wrote: >>> >>> OK, those files contain basically the same information as an isosurface >>> -- vertex list, vertex color, vertex value (several!), and triangles list. >>> That's all you need to do just about anything in Jmol with a surface. Can't >>> create a JVXL file. But if this data really is isosurface data, then it >>> might be possible to get the developers of that program to also output cube >>> data instead of this final form. >>> >>> Bob >>> >>> >>> On Mon, Nov 10, 2008 at 11:06 AM, Robert Hanson <ha...@st...>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 >>>> >>> >>> >>> >>> -- >>> 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 >>> >>> >>> >>> ------------------------------------------------------------------------- >>> 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 >> >> >> >> ------------------------------------------------------------------------- >> 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 > -- 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 |