Karl, the .jmol file is simply a ZIP file. The WRITE command is configured to automatically get the type of file from common extensions -- .GIF, .PNG, .SPT, .WRL, etc., and .JMOL. But it's just a ZIP file. It contains:
- a manifest file that tells Jmol which file the "autoload" script is in. - a PNG image of the state (which also contains the script, by the way). - all files necessary. (If that's not the case, we have a bug.) The script file is stripped of all file path references -- they are changed to "./", so all the files must be in the current directory, which for a ZIP file means within the zip file itself. Here are a couple of examples: http://chemapps.stolaf.edu/jmol/docs/examples-11/data/test1.jmol http://chemapps.stolaf.edu/jmol/docs/examples-11/data/test.zip We added the .jmol extension because then on a Windows machine you can set the Jmol application up to be the default reader for those, and files sent by email or via links can be opened directly into Jmol. Bob On Fri, Aug 20, 2010 at 9:34 AM, Karl Oberholser <oberh...@messiah.edu>wrote: > Bob, > I had missed the capability of writing a data file as a zip file > (xxx.jmol). I suppose that after doing the compare command on two protein > molecules that you could write a "xxx.jmol" file rather than a "xxx.pdb" > file"? When I do this operation, I use 'load' and 'load append' putting the > protein data in two different frames, but when the "xxx.pdb" file is written > the data is present in one frame as two models. What is the structure of > the data in the "xxx.jmol"? > > Karl > > > > Karl M. Oberholser, Ph.D. Phone: > Professor of Chemistry Voice: 717-766-0512 > Chemistry & Biochemistry Dept. Fax: 717-691-6046 > Messiah College e-mail: oberh...@messiah.edu > P.O. Box 3049 > One College Avenue > Grantham, Pa 17027 > > > >>> Robert Hanson <hans...@stolaf.edu> 08/19/10 12:39 PM >>> > (typo -- "jmol" extension is just a Jmol equivalent of "zip" the way "jar" > is for Java) > > > On Thu, Aug 19, 2010 at 11:37 AM, Robert Hanson <hans...@stolaf.edu> > wrote: > > > In case that was too cryptic. > > > > 0) get the picture you want. > > 1) create the jvxl file: write "xxx.jvxl" > > 2) replace the surface with the jvxl equivalent: isosurface "xxx.jvxl" > > 3) create a manifested zip file: write "xxx.jmol" > > > > Then when you load xxx.jmol, Jmol should load the file, load the surface, > > and display it all exactly the way you had it. If it doesn't, let me > know. > > > > Bob > > > > > > > > On Thu, Aug 19, 2010 at 11:30 AM, Robert Hanson <hans...@stolaf.edu > >wrote: > > > >> write xxx.zip > >> > >> > >> > >> > >> On Mon, Aug 16, 2010 at 4:44 AM, <jaime.prilu...@weizmann.ac.il> wrote: > >> > >>> Dear Jmol, > >>> > >>> Is there a way to save Jmol state with the pre-calculated surface? > >>> > >>> We can save the Jmol state, and render the structure with the same > >>> look, orientation, etc. However, if the state contains a surface > >>> calculation, the surface is recalculated again on load. > >>> > >>> On the other side, I can save to .jvxl the surface alone ... > >>> > >>> Can we combine both? > >>> Or the option is to reload state and then load jvxl? > >>> > >>> Thanks, > >>> Jaim > >>> -- > >>> Dr Jaime Prilusky | > jaime.prilu...@weizmann.ac.il > >>> Head Bioinformatics | > >>> R&D Bioinformatics and Data Management | > >>> Department of Biological Services | > >>> Weizmann Institute of Science | fax: 972-8-9344113 > >>> 76100 Rehovot - Israel | tel: 972-8-9344959 > >>> > >>> OCA, http://oca.weizmann.ac.il (the protein structure/function > >>> database) > >>> Proteopedia, http://proteopedia.org (because life has more than 2D) > >>> > ------------------------------------------------------------------------ > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> This SF.net email is sponsored by > >>> > >>> Make an app they can't live without > >>> Enter the BlackBerry Developer Challenge > >>> http://p.sf.net/sfu/RIM-dev2dev > >>> _______________________________________________ > >>> Jmol-users mailing list > >>> Jmol-users@lists.sourceforge.net > >>> 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 > > > > > > -- > 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
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