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 <[email protected]>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
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
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