From: Michael E. <ev...@il...> - 2013-06-17 23:22:36
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Eric, You should give JSmol a try! Depending somewhat on the complexity of your code, I think you'll find the switch pretty easy... :-) For me a few mass find/replaces did the trick. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Sun, Jun 16, 2013 at 10:16 PM, Eric Martz <em...@mi...>wrote: > I have today released a new version of FirstGlance in Jmol (1.95) with > several enhancements. http://firstglance.jmol.org as always. This > supercedes version 1.9 released April 23 of this year, and version 1.92 > released May 5. > > You can now see the *Crystal Contacts* to the asymmetric unit, and the *Unit > Cell*, each with one click (Tools tab). Crystal contacts may affect > conformation, temperature (B factor), and stabilize protruding moieties. > Examples of each are given in the Help panel. > > Slab has been enhanced with a checkbox that shows the rear of the molecule > (so only the front is cut away). Now you can see the *inside of a cavity > or channel*. Example PDB codes are linked to the Slab Help panel. > > In the Molecule Information Tab, *hydrogen* atoms are counted, and an > estimate is made of whether all hydrogens are present, or only hydrogens on > polar atoms. > > Secondary structure now reports the *percentage of amino acids in helices > and strands*. > > Atoms with *alternate locations*, when they occur, are now reported in > the Molecule Information Tab, with a tool to find them. Examples: 3hyd, > 1bsz. > > The Hide and Find tools are now available in all four tabs (at the > bottom). Thanks to Frieda Reichsman for this suggestion. > > A more complete list is here: > http://firstglance.jmol.org/versions.htm > > If you have suggestions for improvements, please do let me know! > > There are undoubtedly bugs. Please report anything that looks dubious, > being sure to include the PDB code you were using. > > Eric > > P.S. I have not undertaken a JSmol version yet. > ** > > ** /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > 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, used by Nature - > http://firstglance.jmol.org > 3D 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 > Atlas of Macromolecules: http://atlas.molviz.org > Interactive Molecules in Public Spaces http://MolecularPlayground.Org > <http://molecularplayground.org/>Workshops: http://workshops.molviz.org > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |