OK. I see what is happening. People may not want to do this, but.
Safari Preferences>security>Manage website settings. I had to set the local
documents to “run in unsafe mode”. Then the jmol applet loads from a local
file.
On Nov 25, 2013, at 5:17 PM, Robert Hanson <[email protected]> wrote:
> So the secret is how to get the local file system into the allowed web sites
> list. OK. Pray tell.....
>
>
> On Mon, Nov 25, 2013 at 4:15 PM, Philip Bays <[email protected]> wrote:
> Bob:
> I did find that in Safari Preferences>security>java there is a list of
> trusted sites. Somehow I was able to get Local documents onto that list. So
> JSmol does work at this point, I think. I will look at the new release and
> see how that works. Unfortuanetly, preparing for company at the moment.
>
>
> On Nov 25, 2013, at 5:05 PM, Robert Hanson <[email protected]> wrote:
>
>> easy fix - it's in the applet's menu.
>>
>>
>> On Mon, Nov 25, 2013 at 3:05 PM, <[email protected]> wrote:
>> Good to see that the Java certification issue seems to be sorted.
>>
>> With respect to bug-fix requests, I'm still experiencing the following
>> problem:
>>
>> calling:
>>
>> load =3fsx.cif filter "ASSEMBLY 1"
>>
>> works in the Java application *only*. That is, it
>> causes the Java Applet to 'hang' and produces the following error using
>> JSmol:
>>
>> File Error:ERROR creating model: TypeError:
>> biomolecules.get(...).get(...) is null
>> script ERROR: ERROR creating model: TypeError:
>> biomolecules.get(...).get(...) is null
>> ----
>> load "=3fsx.cif" filter >> "ASSEMBLY 1" <<
>>
>> I'm seeing this whereever I try it (various machines, various web sites,
>> and with various pdb mmcifs)
>> so I suspect it is a genuine bug?
>>
>> Cheers
>>
>> Simon
>>
>> NB. load =3fsx.cif filter "ASSEMBLY 2" works fine - its just the
>> '1_555' assembly that hangs
>>
>>
>>
>> Quoting Robert Hanson <[email protected]>:
>>
>> > Seems to me it's been over a year since we went Jmol 13, and in that time
>> > all the business of JSmol and Java issues and integration with JSpecView
>> > and JSME have come to pass. Time for a new major version number, I think.
>> >
>> > I would like to retire Jmol 13.3 and 13.2 and release Jmol 14.0 by the end
>> > of the week. Please send all bug fix requests as soon as possible directly
>> > to this list.
>> >
>> > Very latest, with fixes for mouse wheel binding, load monitor transparency,
>> > load() function security, local JNLP applet loading, new _use _jar and _j2s
>> > URL options, but not Safari local applet loading, can be found at
>> >
>> > http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.25.zip
>> >
>> > 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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>>
>> --
>> 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
>>
>> ------------------------------------------------------------------------------
>> Shape the Mobile Experience: Free Subscription
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>> conversations that shape the rapidly evolving mobile landscape. Sign up now.
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>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> [email protected]
>
>
>
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>
>
>
> --
> 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
>
> ------------------------------------------------------------------------------
> Shape the Mobile Experience: Free Subscription
> Software experts and developers: Be at the forefront of tech innovation.
> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up now.
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
[email protected]
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