[Molvis-list] FirstGlance in Jmol: Enhanced

[Eric Martz]

Dear Malcolm,

As far as I know, the web page does not control how Java is enabled. 
I think what you did is correct, and FirstGlance will run with much 
less fuss next time on your computer. However Java itself (or the 
operating system) may now ask you for confirmation to use Java 
(because of its many past security problems) every time you open the 
browser for a new session. That happens on my Mac OS 10.6.8. But once 
I OK Java, I don't have to approve Java again until I completely 
close the browser session and start a new one. An option may pop up 
to approve using Java on a particular website (such as FirstGlance). 
In my opinion all this is good -- because users need to be warned 
when they find themselves at an unknown website that may be 
malicious. Enabling Java at such a site could possibly lead to damage 
to your computer or theft of private information.

Did you notice the red link below the molecule "Java Security"? It 
recommends a strategy for maximum safety. I added that recently.

If you have any suggestions to improve the design of FirstGlance, I 
am interested, of course!

Best regards, Eric



At 4/24/13, you wrote:
>Eric,
>I appreciate all the effort you put into education. Thank you.
>
>The one suggestion I would have has to do with Java. I have some 
>Jmol pages that when the browser is not set up to view it, some text 
>comes up that allows me to click on it and get the java running. On 
>FirstGlance, I saw a yellow page that sent me to a new site and a 
>few links later, I could turn it on. Then I came back to FirstGlance 
>and it worked. I think there is a way to set up these pages so that 
>once Java is enabled, it will always work. A colleague of mine told 
>me how to do this for my Jmol tutorials, but I have not gone back to 
>redo all my pages. Perhaps you already know what this is.
>
>Anyway, I was able to play around with the tabs and got them to work.
>
>Malcolm
>
>
>
>On Apr 23, 2013, at 9:12 PM, Eric Martz wrote:
>
> > I have today released a new version of FirstGlance in Jmol with 
> many enhancements.
> > http://firstglance.jmol.org as always.
> >
> > Formerly there was a single upper left control panel. Now there 
> are 4 tabs in the control panel: Molecule (labeled with the PDB 
> code), Views, Tools, and Resources.
> >
> > The Molecule tab is entirely new. It digests and summarizes a lot 
> of information from the PDB file. Resolution and Free R are 
> "graded" to assist those who are not structural biologists in 
> interpreting them. Missing residues are reported chain by chain, 
> including counts of charged residues that are missing.
> >
> > The initial view has been modified to include "empty baskets" in 
> the regions where residues present in the crystal are missing in 
> the model due to disorder. Thus you can no longer be unaware when 
> there are missing residues.
> >
> > There is a clickable list of ligands and non-standard residues 
> with their full names.
> >
> > The "Find" tool now supports finding sequences, e.g. sequence=rgd 
> will highlight (and count) all Arg Gly Asp sequences present in all 
> chains. Ditto for nucleotide sequences.
> >
> > The biological unit (quaternary structure) is more readily 
> available and more help is provided.
> >
> > Former versions of FirstGlance reported no counts. This version 
> reports counts of many things, including chains, amino acids, 
> nucleotides (total and per chain), lengths of chains, missing 
> residues, missing charged residues, numbers of each 
> ligand/non-standard residue, disulfide bonds, and anything found 
> with the "Find" tool.
> >
> > There are many new convenience features.
> >
> > A more complete list of enhancements 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
> >
> > Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
> > FirstGlance, used by Nature - http://firstglance.jmol.org
> > 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
> > Biochem 3D Education Resources 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
> > Workshops: http://workshops.molviz.org
> > - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> >
> > _______________________________________________
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> > Molvis-list at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/molvis-list
>
>________________________________________________________
>A. Malcolm Campbell, Ph.D.
>Professor of Biology
>Director, James G. Martin Genomics Program
>Davidson College
>Founding Director of GCAT (www.bio.davidson.edu/GCAT )
>
>Box 7118 (US Mail)
>209 Ridge Road (shipping)
>Davidson, NC  28035
>704-894-2692 (phone)
>704-894-2512 (fax)
>www.bio.davidson.edu/campbell
>
>
>
>
>
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/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://Martz.MolviZ.Org

Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
FirstGlance, used by Nature - http://firstglance.jmol.org
3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
Biochem 3D Education Resources 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
Workshops: http://workshops.molviz.org
- - - - - - - - - - - - - - - - - - - - - - - - - - - */