Jmol.___JmolVersion="14.3.9_2014.11.25"
new feature: isosurface "==1blu"
-- difference map fo-fc
-- defaults to sigma=3
-- automatically implements SIGN option
new feature: isosurface RMSD (same as SIGMA)
bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.9_2014.11.25.zip
On Tue, Nov 25, 2014 at 12:01 AM, Dale Tronrud <[email protected]>
wrote:
>
> Thanks a bunch. Yes, the usual practice is to contour at +_3 sigma,
> but I can add SIGN to get both.
>
> Dale
>
> P.S. If this were the CCP4BB I'd argue about the misuse of the word
> "sigma" when all you are talking about is a simple rms but I doubt I
> could get you to change your syntax at this point. ;-)
>
>
> On 11/24/2014 6:53 PM, Robert Hanson wrote:
> > Jmol.___JmolVersion="14.3.9_2014.11.24"
> >
> > new feature: isosurface "==1blu" -- difference map; defaults to sigma=3
> >
> >
> >
> > On Mon, Nov 24, 2014 at 8:39 PM, Robert Hanson <[email protected]
> > <mailto:[email protected]>> wrote:
> >
> > (how many sigma?)
> >
> > On Mon, Nov 24, 2014 at 8:24 PM, Robert Hanson <[email protected]
> > <mailto:[email protected]>> wrote:
> >
> > How do you set the cutoff for that?
> >
> > Note that you can use the full call directly:
> >
> > isosurface "http://eds.bmc.uu.se/eds/dfs/bl/1blu/1blu_diff.omap";
> >
> >
> >
> > On Mon, Nov 24, 2014 at 5:01 PM, Dale Tronrud
> > <[email protected] <mailto:[email protected]>> wrote:
> >
> >
> > I would like to display both the 2Fo-Fc and Fo-Fc maps
> > from the
> > Electron Density Server at the same time. When I issue the
> > command
> > "ISOSURFACE =3EOJ" for example, I get the 2Fo-Fc map, but I
> > don't see
> > a syntax for getting the difference map.
> >
> > If I could change edsUrlFormat to change the downloaded
> > file name I
> > expect that ISOSURFACE would download the map I want, but I
> > don't see
> > how to access such jsmol internals while within a jsmol script.
> >
> > Any advice on how to do this would be appreciated.
> >
> > Dale Tronrud
> >
> > FYI: The value of edsUrlFormat that I want is
> > "http://eds/bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE_diff.omap";.
> >
> >
>
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> >
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > Chair, Department of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > 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
> > Larson-Anderson Professor of Chemistry
> > Chair, Department of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > 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
> > Larson-Anderson Professor of Chemistry
> > Chair, Department of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > 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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> >
> >
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> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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