isosurface problem is fixed. It's the same reason I pulled 14.1.14:
x = 3
select atomno=x
does not work.
On Mon, Apr 28, 2014 at 11:43 AM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> Sorry but I have other things I must do today so
> I won't have time to find what is the problem
> with isosurfaces. Please go ahead with 14.x.14.
>
> Empty baskets (my term and my invention) show
> where residues are missing in the model, due to
> disorder, even tho present in the crystallized
> protein. For an example, view 1d66 in
> FirstGlance. Read the Intro help panel which
> explains at the top. Then in the Molecule
> Information control panel (top left), click on
> Missing Residues for details. As it says, 77% of
> X-ray models have missing residues. Most people
> who look at those models never realize, so I'm
> trying to make it obvious. If you're looking at
> charge distribution or conservation patterns,
> having missing residues could be misleading!
>
> Eric
>
> At 4/28/14, you wrote:
> >"I released this version with Jmol 14.0.13 because of some problem
> >with isosurfaces in 14.0.14. My prior code (for "empty baskets" to
> >show where residues are missing from the model due, usually, to
> >crystallographic disorder) works in 14.0.13 but not in 14.0.14. The
> >simple isosurface command works fine in 14.0.14 so I will need to
> >spend time to determine what sequence of script commands in
> >FirstGlance causes it to fail."
> >
> >Yes, please do. I was about to release 14.1.14
> >(again!) but will wait until this evening to do
> >that if you can get back to me with this.
> >
> >What are these "empty baskets"? Please point me to where they are
> utilized.
> >
> >Bob
> >
> >
> >
> >
> >
> >On Sun, Apr 27, 2014 at 11:35 PM, Eric Martz
> ><<mailto:[email protected]>[email protected]> wrote:
> >I have today released FirstGlance in Jmol version 2.00. As always,
> >
> ><http://FirstGlance.Jmol.Org>http://FirstGlance.Jmol.Org
> >
> >This version needs no Java. By default, it uses JSmol (no Java), so
> >it can run on computers where Java is not installed, or is
> >unavailable (such as iPads).
> >
> >It can also run with Java, which greatly improves speed, performance,
> >and smoothness of rotation of the molecule.
> >
> >There is a new Preferences tab, in which you can set it to default to
> >using Java. Installing and enabling Java in various web browsers has
> >become more and more challenging, so detailed instructions are linked
> >to the Preferences tab.
> >
> >This version has no new capabilities for molecular display. It mainly
> >makes using JSmol without Java much more user friendly (I hope!).
> >
> >I released this version with Jmol 14.0.13 because of some problem
> >with isosurfaces in 14.0.14. My prior code (for "empty baskets" to
> >show where residues are missing from the model due, usually, to
> >crystallographic disorder) works in 14.0.13 but not in 14.0.14. The
> >simple isosurface command works fine in 14.0.14 so I will need to
> >spend time to determine what sequence of script commands in
> >FirstGlance causes it to fail.
> >
> >Feedback welcome. There is always much more to do but feedback can
> >alert me to issues I've overlooked, and help me set priorities.
> >
> >Eric
> >
> >
> >/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >Eric Martz, Professor Emeritus, Dept Microbiology
> >U Mass, Amherst -- <http://Martz.MolviZ.Org>http://Martz.MolviZ.Org
> >
> >Top Five 3D MolVis Technologies <http://Top5.MolviZ.Org>
> http://Top5.MolviZ.Org
> >FirstGlance: 3D Views in Nature -
> ><http://firstglance.jmol.org>http://firstglance.jmol.org
> >3D Protein Wiki with Scene-Authoring Tools
> ><http://Proteopedia.Org>http://Proteopedia.Org
> >Biochem 3D Education Resources <http://MolviZ.org>http://MolviZ.org
> >ConSurf - Find Conserved Patches in Proteins:
> ><http://consurf.tau.ac.il>http://consurf.tau.ac.il
> >Atlas of Macromolecules: <http://atlas.molviz.org>http://atlas.molviz.org
> >Interactive Molecules in Public Spaces
> ><http://MolecularPlayground.Org>http://MolecularPlayground.Org
> >Workshops: <http://workshops.molviz.org>http://workshops.molviz.org
> >- - - - - - - - - - - - - - - - - - - - - - - - - - - */
> >
> >
>
> >------------------------------------------------------------------------------
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> >
> >--
> >Robert M. Hanson
> >Larson-Anderson Professor of Chemistry
> >St. Olaf College
> >Northfield, MN
> ><http://www.stolaf.edu/people/hansonr>
> 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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--
Robert M. Hanson
Larson-Anderson Professor 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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