Yes, I see it, too. It appears that generating the files for JSmol 13.2
after generating them for 13.3 creates a mixed set of files. I have to be
more careful...
On Wed, Sep 18, 2013 at 4:59 PM, Otis Rothenberger <[email protected]>wrote:
> Bob,
>
> If I go to your test page, I see the line problem. It seems to start with
> a pdb load. After it starts, all loads seem to be line loads. Your test
> page indicates 13.3.6_dev_2013.09.016. I don't see this when I load files
> from RCSB on the ISU server. For what it's worth, my version number comes
> up 13.3.6_dev_2013.09.16 - note 016 vs 16.
>
> I'm using Mac OS X 10.7.5. Safari 6.0.5 (7536.30.1).
>
> I do not see the problem with Chrome for either page.
>
> 13.3.6_dev_2013.09.16 seems to load very slowly on the ISU server. They
> may be having problems today. I do not have the newer versions on the
> chemagic server at this point.
>
> As far as reproducibility is concerned, it seems random. PDB's seem more
> likely to start it, but that's not exclusive.
>
> On my server, I'm loading PDB's with load =id. For other models, I'm not
> loading directly from the remote source. I always go via AJAX and a script
> on my server.
>
> Otis
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
> On Sep 18, 2013, at 3:26 PM, Robert Hanson wrote:
>
> what an evil bug. Yes, probably due to the update. Fundamentally this had
> to do with how Safari was translating characters into integers.
>
> Please test ASAP and give details about which browsers exactly. Detail for
> reproduction, please.
>
>
> On Tue, Sep 17, 2013 at 7:20 PM, Otis Rothenberger
> <[email protected]>wrote:
>
>> Phil,
>>
>> OK, I see it on Bob's page. I've been testing on my page at:
>>
>> http://chemistry.illinoisstate.edu/osrothen/JSmolVMK.htm
>>
>> I haven't seen the lines there yet. Try it per the load commands for the
>> script field on the main page:
>>
>> loadpdb
>> searchpdb
>>
>> I'm on Safari 6.0.5 (7536.30.1)
>>
>>
>> I haven't yet document the read/write commands, but the are
>>
>> loadloc
>> saveloc
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> [email protected]
>> http://chemagic.com
>>
>>
>>
>>
>> On Sep 17, 2013, at 8:05 PM, Bays Philip wrote:
>>
>> Try loading a protein from the right-hand column. What do you see?
>> Remember when we had the odd display of simply lines on the screen several
>> weeks ago? I see it again. You may have to load several structures before
>> the problem shows up. Once it appears, you have to reload the page to get
>> rid of it.
>>
>> Now, I updated the OS today to 10.8.5 and that also updates Safari
>> (6.0.5) so the problem could be there.
>>
>>
>> On Sep 17, 2013, at 7:41 PM, Otis Rothenberger <[email protected]>
>> wrote:
>>
>> Hi Phil,
>>
>> I thought the missing name was normal. When I wrote my friend today, I
>> had to explain that after selecting the file, he had to click the load
>> button!
>>
>> I'm not sure I know what you mean by the lines issue. What am I looking
>> for in Safari with this issue?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> [email protected]
>> http://chemagic.com
>>
>>
>>
>>
>> On Sep 17, 2013, at 6:19 PM, Philip Bays wrote:
>>
>> Bob:
>>
>> On a Mac using the latest OS (10.8.5)
>>
>> Firefox works fine to load and write files; there seems to be no choice
>> where they get downloaded, though I can control that in the browser
>> preferences. I note that the name of the file selected to load is given in
>> the dialog.
>>
>> In Safari there are a couple of issues. The name is not given when the
>> file is chosen. More importantly, we are back to the lines issue. I have
>> cleared the browser cache, and, in fact, disabled it. Perhaps Otis can
>> confirm that glitch??
>>
>>
>> On Sep 17, 2013, at 5:54 PM, Robert Hanson <[email protected]> wrote:
>>
>> Used to be that it required the signed applet to read and write files
>> locally. Well, well, what do you know? I'm liking HTML5 more and more. The
>> following commands, previously for the signed applet only, now work in
>> JSmol/HTML5.
>>
>> load ? x = load("?")
>>
>> write file ?
>>
>> write xxx.jpg write xxx.png write PNGJ xxx.png
>> write PNGJ 500 500 "xxx.png"
>> write xxx.zip write xxx.jmol
>>
>> write xxx.pdb write xxx.mol write xxx.v2000
>> write xxx.v3000 write xxx.xyz
>>
>>
>> What's especially satisfying for me is that the loading is done
>> asynchronously. I had thought that would be extremely difficult to do -- to
>> pause a running script of however many levels of depth and deep into
>> however many function calls while an asynchronous file load was happening,
>> then restart upon completion at the right place. Well, guess what? It was
>> only moderately difficult! The HTML5 FileReader API is great. [
>> http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support
>> across browsers (http://caniuse.com/#feat=filereader), although one
>> cannot go back very far in time.
>>
>> Writing files to disk still requires "reflecting" the data from
>> Info.serverUrl, but I'm optimistic (based on
>> http://caniuse.com/filesystem) that the HTML5 FileWriter API will
>> continue to be introduced and at some point will allow us to get rid of the
>> need of a server for local file writing. Certainly what we have now is
>> close to ideal.
>>
>> Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>>
>> http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.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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>>
>> Philip Bays
>> Emeritus Professor of Chemistry
>> Saint Mary's College
>> Notre Dame, IN 46556
>> [email protected]
>>
>>
>>
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>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> 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
>
> ------------------------------------------------------------------------------
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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
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