Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[J. Bays]

Well Wavefunction has such a database, but it is not available to
non-Spartan users, as far as I know.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On Aug 24, 2016, at 10:39 AM, Jennifer L. Muzyka 
wrote:

iSpartan has something like that built into their app rather than
calculating things on the fly.  I’m not aware of any other database that
has the information you’re looking for, Bob.
Jennifer



Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Aug 24, 2016, at 10:34 AM, Robert Hanson  wrote:

I mean a database of common organic compounds, with molecular orbitals.
Spartan files or Gaussian output -- that sort of thing.
​
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Re: [Jmol-users] incomplete cartoons in Calpha-only files

[J. Bays]

What version of jmol are you using?  Today’s or the one from the 27th?  The 
latter had issues with protein structures.


> On Jun 30, 2016, at 11:20 AM, Herráez Sánchez Ángel  
> wrote:
> 
> Sorry!
> I realize now that this could be due to Proteopeida now using mmCIF files 
> instead of PDB files
> Not sure that is the cause, since I did not invent the idea of removed 
> header, I saw that for sure -- maybe with some other example.
> 
> (This bug was discovered while we were investigating other issues -strands 
> broken into triangles- so I have mixed memories)
> 
> 
> De: Herráez Sánchez Ángel >
> Enviado: jueves, 30 de junio de 2016 17:07
> Para: jmol-users list
> Asunto: [Jmol-users] incomplete cartoons in Calpha-only files
>  
> We are seeing a problem in Proteopedia that apparently was not present before 
> (it is unlikely that it had went unnoticed). I wonder if it is the result of 
> upgrade to recent Jmol versions. (14.4 at least, 14.6 for sure) 
> I am still seeing it with today's release 14.6.0_2016.06.30
> It affects both JSmol and Jmol application.
> 
> Ppedia loads PDB files from its own server, and it is using copies that have 
> removed the header section, including HELIX and SHEET records.
> 
> The initial load of that pdb file is done with Calpha-only and P-only, using 
> this filter:
> 
> load  models ({0}) http://proteopedia.org/cgi-bin/getlateststructure?1wm1.gz 
>  filter 
> "*.CA,*.P|HETATM,![HOH]";
> 
> Under this setup, "select protein; cartoon only" renders nice helices, but 
> beta strands fail to display as ribbons --just a trace like for unordered 
> segments.
> 
> When loading the full model (i.e. without the filter) all works well.
> 
> So this is a failure of Jmol to identify beta strands/cartoons when only 
> Calpha is present and no SHEET records in the file.
> 
> "calculate structure" does not help
> 
> Could this have been a change in behaviour across versions?
> Of course a possible solution is to avoid the removal of SHEET records in the 
> local pdb file copy, but I think this used to work previously.
> 
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Re: [Jmol-users] page-developer request - Jmol Unplugged

[J. Bays]

Bob:
Here is a link to a directory that contains stereochemistry and spectroscopy 
tutorials which our students have found helpful.  It is small and runs without 
network connection.  The index file contains the links to the two sets of 
tutorials, or you can just open them from the appropriately titled .htm files.

https://dl.dropboxusercontent.com/u/17514932/PBays.zip 



> On Jun 28, 2016, at 9:00 AM, Robert Hanson  wrote:
> 
> Jmol page developers,
> 
> Today I am giving a workshop on the use of Jmol in general and inorganic 
> chemistry. Tomorrow the subject is organic chemistry, and Thursday it is 
> physical chemistry. These workshops are at the Universidad Mayor San Simón, 
> in Cochabama, Bolivia. Please feel free to come and help me out!
> 
> While there is widespread fast internet in Bolivia, there are certainly times 
> and places where it is not available. (One of those places is an auditorium 
> where I am giving another presentation tomorrow.)
> 
> I have an idea that will change the way Jmol is used in many parts of the 
> world. It will open up opportunities for millions of students and thousands 
> of professors and high-school teachers to use Jmol. It's simple. I'm not sure 
> exactly what to call it, but for now I am calling it "Jmol Unplugged". Here 
> is the idea:
> 
> Somewhere - possibly SourceForge - we create a site where people can upload 
> fully contained web site "packages" that amount to stand-alone web 
> applications. For example, I just created this directory:
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites 
> 
> 
> where we find
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/coolMolecules.zip 
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/orbitals.zip 
> 
> 
> These are the fully-contained fully operational JavaScript versions of 
> 
> http://www.stolaf.edu/depts/chemistry/mo/struc 
>  
> http://chemapps.stolaf.edu/jmol/orbitals 
>  
> 
> They can be downloaded to a laptop and -- provided the browser is set up for 
> local file reading -- they will run totally disconnected from the web.
> 
> The conditions for curation would be something like this:
> 
> 1)  For the most part the site must work without an internet connection. It 
> would be fine if it still has a few links to external pages that are not 
> critical to the function of the site. But the primary function of the site 
> would have to be self-contained. That means no use of NCI Resolver, PubChem, 
> or RCSB, for example.
> 
> 2) The site is JavaScript only. Or, at least it is either Java-only or 
> JS-only, and if it is Java only, that is clearly indicated in its file name. 
> 
> 3) The contributor understands that they are giving away their site. Someone 
> can now take it, change it, put it up somewhere on their own. Whatever. Maybe 
> there's a licensing agreement that has to be worked out. I don't know.
> 
> Obviously we would  need some sort of introductory page with descriptions of 
> the site packages. I think that would be a Wiki -- maybe even Wikipedia? Not 
> sure about that. 
> 
> We would have to think about whether we want to have these totally 
> self-contained, with the  j2s directory, or not. My inclination is that we DO 
> have them contain the j2s directory so that no changes to Jmol affect the 
> site. But there might be other options there. I don't want to make this more 
> complicated than it has to be.
> 
> I think there's a publication in this for anyone who wants to help organize 
> it and get it off the ground. It will take some effort to standardize it, 
> figure it out, and curate it.
> 
> Right now I am asking for anyone who wants to contribute their work to send 
> me a link to a zip file that, when opened, contains your site and fits these 
> criteria. 
> 
> If you would let me use your site in my workshops and put them up temporarily 
> at chemapps.stolaf.edu , send me a link today.
> 
> Thank you!
> 
> Bob
> 
> -- 
> 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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Re: [Jmol-users] JmolApplet.jar

[J. Bays]

That would be fine with me. First thing I do with a release is delete all
things Java.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On May 18, 2016, at 1:05 AM, Robert Hanson  wrote:

Two questions:

1. What would you think of dropping JmolApplet.jar from the
distribution?
2. How about JmolAppletSigned.jar?

Could these, perhaps be in a separate zip for download, perhaps
JmolAppletJava.zip?


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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[Jmol-users] Flat structures

[J. Bays]

I have been trying to look at the structures of various cancer drugs.   Most 
download like taxol, as flat structures.  I realize that I can do a 
minimization in Jmol to improve that, but it is slow on my computers.   I have 
been exporting them as mol files and then minimizing them Student Spartan which 
is very fast.   I then reload the resultant .mol file into jmol.  

The questions I keep asking myself are of what use are these flat structures 
and why are they in the databases in that form?  Anybody know?



J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu






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Re: [Jmol-users] New iPad

[J. Bays]

When you buy one of these, what storage do you get:32, 64, 128..?

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

> On Apr 22, 2016, at 6:11 PM, Otis Rothenberger  wrote:
>
> I know I obsess about Jmol and tablets on this list, but my lifestyle these 
> days involves basically walking or bicycling as my local travel mode. Whether 
> for  bird photography work or Jmol work, I often find myself working in the 
> Anna Maria Island library, and my laptop is not an option - hence the more 
> portable tablet.
>
> I just purchased the small iPad Pro, and there are some noteworthy 
> improvements in Jmol response worth mentioning:
>
> 1) Jmol models are now very motion responsive in Safari AND Chrome AND the 
> in-app browsers I’ve checked.
>
> 2) The application Textastic Code Editor has been re-written for Pro. 
> Basically, you can now do the following:
>
> A) Store your entire site in the App. With the cloud, your current 
> developmental site is always available - home, laptop, and iPad. While stored 
> locally, files sync quickly when you’re on line.
>
> B) Quickly preview a page in the in Textastic App browser (Jmol very motion 
> responsive) OR Safari itself in a new iPad Safari localhost. The latter makes 
> full use of tabs, local storage, etc. You’re in Safari with a local iPad site.
>
> C) While the localhost does not run server scripts, it does allow contact 
> with remote server scripts (read and write) when you’re on line, so if your 
> page uses full url’s for server calls, you're in business.
>
> If you try any of this on a Mac or an iPad, Apple is case sensitive when if 
> comes to the file names on the localhost.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>
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[Jmol-users] Nucleic acids

[J. Bays]

Never mind. Figured it out.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

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Re: [Jmol-users] Ligands

[J. Bays]

Yes. Thanks. I am working on something for our biochemist.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

> On Mar 30, 2016, at 5:44 PM, Otis Rothenberger  wrote:
>
> Phil,
>
> I’m a little molecule guy, but see if this page has what you want:
>
> http://chemapps.stolaf.edu/pe/protexpl/htm/seleccmd.htm
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>> On Mar 30, 2016, at 4:30 PM, Philip Bays  wrote:
>>
>> Can JSmol pick out and display ligands in proteins?  What is the script for 
>> that?
>>
>> Phil
>>
>> Philip Bays
>> Emeritus Professor of Chemistry
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[J. Bays]

OK.  I have looked at it again.  PubChem works but I am getting the invalid 
message from RCSB.  I am running on Mac OS X the latest version (before today). 
  I have it on my home server and accessing it as a localhost file or from my 
laptop on the local network.  I have cleared cache.  But I am also seeing this 
on the release of the 13th.  so I am not sure that it the software or me.




> On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
> 
> I am not seeing that. Others?
> ​
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Re: [Jmol-users] new InChI option

[J. Bays]

Just a question. Taxol is pretty a complex structure. Are you able to
calculate and load others of equal complexity without crashing? Perhaps the
error occurs in the calc part.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On Mar 8, 2016, at 6:22 PM, Otis Rothenberger  wrote:

Bob,

I'm using the approach on github. The molfile and the calculated inchi are
in globals per their suggestions. For testing, I set the globals to ""
before each model load. This led to erroneous matches at the taxol break -
i.e. "" == "".

I'm seeing all kinds of irratic behavior all related to taxol. Here's
what's pretty constant:

1) Things work pretty well if you don't load taxol!
2) Loading taxol results in:

a) Taxol works.
b) The next model load works (usually).
c) Any model (usually) breaks it on a third load. Why 3rd load after the
taxol bomb?

3) The ChemWriter demo at github does not like Taxol either - loaded via
paste Jmol taxol molfile.

4) When the Jmol page breaks with Taxol (3rd load, go figure), I'm not
seeing any of the error messages listed in the .mem file. It just breaks.

5) If I wrap the following inchi code (I'm using github suggested code):

calc = InChI.fromMolfile(molfile).trim();

in a try/catch, I get an error when the taxol related 3rd load break
happens:

type error: undefined is not an object (evaluating "a.stack")

I guess I can understand why that taxol molfile breaks the app. It's a
mess. I'd just like to catch this situation before the 3rd load break
starts.

Oh yeah, the first page load after a cache clear almost always throws an
error. This does not break the page however. It just means that you don't
get a page load inchi calculation.

Otis

Sent from my iPad

On Mar 8, 2016, at 3:50 PM, Robert Hanson  wrote:

huh?

On Mon, Mar 7, 2016 at 7:17 PM, Otis Rothenberger 
wrote:

> Bob,
>
> Rats! It’s reporting no difference, but there is a difference. This seems
> to be OK:
>
> $("#log").html(nci==calc ? "no difference" : "check differences?”);
>
> Calc seems to be OK. The problem is what’s printed on the screen for calc.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> > On Mar 7, 2016, at 6:33 PM, Otis Rothenberger 
> wrote:
> >
> > Bob,
> >
> > I think it may be a timing issue with the function below. When I comment
> out the initial JQuery working… html replacements, the page no longer
> “locks.” I don’t think it was really locking. I think those html
> replacements somehow ran after the subsequent code. Which…
> >
> > makes absolutely no sense to me! Nevertheless, it seems to fix the
> problem.
> >
> > function getInChI(app,url) {
> >   //$("#inchi2div").html("working...");
> >   //$("#inchi1div").html("working...");
> >   //$("#log").html("working...");
> >   if (!url) { return; }
> >   nci = Jmol.evaluateVar(jmolApplet0,"show('chemical
> stdinchi')").trim();
> >   $("#inchi2div").html(nci + "(from
> NCI/CADD)");
> >   calc =
> InChI.fromMolfile(Jmol.evaluateVar(jmolApplet0,"write('MOL')")).trim();
> >   $("#inchi1div").html(calc + "(calculated
> in JavaScript)");
> >   $("#log").html(nci==calc ? "no difference" : "check differences?");
> > }
> >
> > Otis
> >
> > --
> > Otis Rothenberger
> > o...@chemagic.org
> > http://chemagic.org
> >
> >> On Mar 7, 2016, at 4:37 PM, Robert Hanson  wrote:
> >>
> >> Otis, note that there is a bug there. If you ask for the models in this
> order:
> >>
> >> $taxol
> >> $morphine
> >>
> >> inchi.js seems to hang and just never respond. Something to do with the
> fact that $taxol is pathologically 2D and not 3D. But
> >>
> >> $taxol
> >> $methanol
> >>
> >> works, until you ask for $morphine. Then it hangs.
> >>
> >> Go figure!
> >>
> >>
> >> Bob
> >>
> >>
> >>
> >>
> >
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

[J. Bays]

That dates us Otis

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

> On Dec 13, 2015, at 4:04 PM, Otis Rothenberger  wrote:
>
> I’m probably not supposed to do this, but the words of Mighty Mouse seem 
> appropriate to yet another Hanson save:
>
> MIGHTY MOUSE THEME SONG
> (Philip Scheib / Marshall Barer) - circa 1955
>
> "Mr. trouble never hangs around,
> when he hears this Mighty sound,
>
> Here I come to save the day!
> That means that Mighty Mouse is on the way!
>
> Yes sir, when there is a wrong to right,
> Mighty Mouse will join the fight!…”
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
>
> --
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Re: [Jmol-users] Fwd: Chrome: rotation unusable in JSmol

[J. Bays]

I see it too. I am running OSX 10.11.2 the latest with Chrome 47, the
latest.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On Dec 10, 2015, at 5:58 PM, Eric Martz  wrote:

In April 2014, Chrome gave the best performance of JSmol: smoothest
rotation and few if any long (~ one minute) pauses during loading of some
modest PDB files (pauses seen in Firefox). I configured FirstGlance in
Jmol, when using JSmol, to recommend Chrome over Firefox. Safari was good.
Internet Explorer was unusably slow with JSmol.

Recently I began to notice jumpier rotation in Chrome, while Firefox and
Safari continue to perform well.

Today I found Chrome to be unable to rotate any molecule (even caffeine) in
JSmol. Although there are brief moments when rotation can be seen, these
are broken by long freezes (> 5 sec) when no rotation can be accomplished.

The problem is worst when the mouse is moved quickly. The molecule freezes
until the mouse is stopped. If you keep moving the mouse, the molecule may
freeze for more than 10 sec. The molecule does rotate with very slow
movements of the mouse.

The problem occurs in OS X, where Chrome has updated to version 47.

Rotation is still quite good in Chrome version 46, which happens to remain
in my Windows 7 and 10 machines, despite version 47 becoming the stable
release on December 1 (

http://googlechromereleases.blogspot.com/search?updated-max=2015-12-01T12:43:00-08:00=10).
Presumably my Windows Chrome will shortly auto-update to 47 and then I will
be very curious about performance.

I tested the OS X beta version of Chrome, version 48, in hopes the problem
would be fixed -- but it remains in Chrome 48 in OS X.

Since Chrome stopped supporting Java on September 1, 2015, Chrome is now
useless for JSmol websites.

We can hope this is a mouse-related bug in Chrome that will be fixed, but
as I mentioned, a fix is not present in the current beta version 48.

This is a sad turn of events! Comments? Suggestions? Insights?

-Eric


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Re: [Jmol-users] try again

[J. Bays]

Paul: I think that is intentional. Try jsmol.htm.  It is the same test
without

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's Collegethe images.
Norte Dame, IN

Sent from my iPad

On Sep 16, 2015, at 9:10 AM, Paul PILLOT  wrote:

Everything works as expected (including localization alerts, filter2D,
fractional coordinates shorthand notation) ! Thanks a lot Bob !

The only remaining glitch is in the test2.htm page that displays 2 still
images in the forefront, having the active molecule displayed ind the
background.
It appears on the two browsers I’ve checked. It doesn’t appear in any of
the other pages I’ve tried so it should only be related to a code in this
specific page.

Here are the images :
- screen shot of the jsmol window : screen_capture.png

- image of the windows as computed per jsmol (image command) :
test2_jsmol.png


-Paul

Le 16-09-2015 à 03:49, Angel Herráez  a écrit :

simple.htm  runs ok now here, without errors and the language is correct
(it
also was before)

On 16 Sep 2015 at 0:00, Robert Hanson wrote:

http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_
2015.09.15-binary.zip

Jmol.___JmolVersion="14.3.16_2015.09.15"



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Re: [Jmol-users] enlarging text in console and script editor windows

[J. Bays]

Yep. Sorry.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On Jul 30, 2015, at 6:36 AM, Robert Hanson hans...@stolaf.edu wrote:

Philip, it's there -- application only. Are you thinking applet?

On Wed, Jul 29, 2015 at 8:40 AM, Philip Bays pb...@saintmarys.edu wrote:

 Is the new Font button missing in the console in ….07.29?


 On Jul 29, 2015, at 5:35 AM, Robert Hanson hans...@stolaf.edu wrote:

 A new [Font] button has been added to the console in Jmol 14.2 and 14.3;
 It allows five different font sizes, from tiny to extra large

 On Tue, Jul 28, 2015 at 6:54 PM, Angel Herráez angel.herr...@uah.es
 wrote:

 Hi Margaret

 I think the answer is no.
 You may copy and paste code to/from a Notepad window -- that's what I
 often use to display text while projecting, it's easy to set the font
 size.




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 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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Northfield, MN
http://www.stolaf.edu/people/hansonr


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Re: [Jmol-users] Safari errors

[J. Bays]

Mavericks and Safari 7. I am off to grandparents day this morning at our
granddaughter's grade school. I will get back to this afternoon.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556

Sent from my iPhone



On Nov 26, 2013, at 8:37 AM, Otis Rothenberger osrot...@chemagic.com
wrote:

Phil,

What version of Safari are you using? For me, Safari iPad and Safari
Desktop became  complete busts after an update to Mavericks and the
Mavericks' Safari - hangs and crashes. For the most part, my problems are
only with scripting. JSmol itself seems OK. Scripts are completely
unpredictable. I'm not even sure I see a pattern.

Otis

-- 
Otis Rothenberger
Department of Chemistry
Illinois State University Normal, IL 61790-4160
http://chemagic.org


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*From*: Philip Bays pb...@saintmarys.edu
*Sent*: Tuesday, November 26, 2013 8:30 AM
*To*: Jmol Jmol jmol-users@lists.sourceforge.net
*Subject*: [Jmol-users] Safari errors

I am looking at your web site the test2. Works fine in firefox. In safari
both jsmol and jmol initially load fine. However, with the jsmol, after
clicking number of links in the database column, the browser hangs and the
page has to be reloaded. In addition, I get the following error alert
popping up with a protein structure:

Javascript
JmolCore.js synchronus binary file transfer is requested but not available.

Clicking OK on this alert allows that structure and a few others to load,
but then it again freezes.


Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



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Re: [Jmol-users] Super Simple JSMol

[J. Bays]

It works on iOS devices, but not OS.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556

Sent from my iPhone



On Nov 6, 2013, at 9:07 AM, Robert Hanson hans...@stolaf.edu wrote:

still a problem? I just tested it with my 1st-gen iPad with Safari and it
was fine.


On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays pb...@saintmarys.edu wrote:

 I have been out of the loop for a while taking care of my wife who has a
 broken and repaired knee cap.   I knew we ought to pay off those gambling
 debts:-)

 I have been looking today at the Super Simple JSmol page (
 http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).

 It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
 However, the HTML5 link does not work in Safari.  A new page is launched
 with the search bar, but the applet (or whatever we are now calling it)
 does not load even after waiting for 10 minutes.

 On the other hand, if I simply open the “Show Error Console” in the
 developers menu in Safari, the HTML5 loads fine.  It is not clear to why
 simply having the console open allows jsmol to load.  Is it a timing thing??

 I see the following error messages in the console for the incident when
 jsmol did not load:

 [Error] Failed to load resource: the server responded with a status of 503
 (Service Unavailable) (get-js, line 0)
 [Error] java.lang.NullPointerException
 (anonymous function) (core.z.js, line 398)
 (anonymous function) (core.z.js, line 2256)
 (anonymous function) (core.z.js, line 2248)
 (anonymous function) (core.z.js, line 2225)
 instantialize (JSmol.min.js, line 343)
 (anonymous function) (core.z.js, line 2223)
 innerTypeInstance (JSmol.min.js, line 358)
 (anonymous function) (core.z.js, line 2192)
 (anonymous function) (core.z.js, line 938)
 (anonymous function) (core.z.js, line 926)
 (anonymous function) (core.z.js, line 917)
 instantialize (JSmol.min.js, line 343)
 (anonymous function) (core.z.js, line 913)
 (anonymous function) (core.z.js, line 506)
 (anonymous function) (core.z.js, line 506)
 (anonymous function) (core.z.js, line 504)
 instantialize (JSmol.min.js, line 343)
 (anonymous function) (core.z.js, line 503)
 __startAppletJS (JSmol.min.js, line 256)
 __nextExecution (JSmol.min.js, line 261)


 Philip Bays
 Emeritus Professor of Chemistry
 Saint Mary's College
 Notre Dame, IN 46556
 pb...@saintmarys.edu




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http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


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Re: [Jmol-users] jsmol issue

[J. Bays]

Yes.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556

Sent from my iPhone



On Sep 7, 2013, at 7:49 AM, Robert Hanson hans...@stolaf.edu wrote:

oh, that's sad to hear. Phil, will you be around in the next hour or so to
help me test? I can work on it for just a short while. What have I done

Bob


On Sat, Sep 7, 2013 at 6:44 AM, Bays Philip pb...@saintmarys.edu wrote:

 No.   Now we are back to the straight line issue.


 On Sep 7, 2013, at 7:40 AM, Robert Hanson hans...@stolaf.edu wrote:

 Nonetheless, if someone with a Mac could check the right-most column links
 of http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm  today, I would
 appreciate it. I changed the PDB links so that if the case one does not
 have binary transfer capability (Safari and Chrome), then  the .gz will
 be removed from requests such as http://www.rcsb.org/pdb/files/1crn.pdb.gz
 so that there is no need for going through the server and doing the binary
 transfer. So at least for those just using RCSB, you don't have to have a
 server piece anyway.

 Bob
 --
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 Larson-Anderson Professor of Chemistry
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


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 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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 Saint Mary's College
 Notre Dame, IN 46556
 pb...@saintmarys.edu



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