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 >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > >------------------------------------------------------------------------------ >"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >Instantly run your Selenium tests across 300+ browser/OS combos. Â Get >unparalleled scalability from the best Selenium testing platform available. >Simple to use. Nothing to install. Get started now for free." ><http://p.sf.net/sfu/SauceLabs>http://p.sf.net/sfu/SauceLabs >_______________________________________________ >Jmol-users mailing list ><mailto:[email protected]>[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > >-- >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 > >------------------------------------------------------------------------------ >"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >Instantly run your Selenium tests across 300+ browser/OS combos. 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