[Jmol-users] jmol-14.3.7_2014.08.25.zip

[Robert Hanson]

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.08.25.zip

Just one minor fix, but what is perhaps interesting here is some low-level
rewriting I did of a couple of core JavaScript implementations of Java
classes (ArrayList, Hashtable) as well as the main j2sjmol.js library code
that looks like it is speeding up some processes by up to 10-15%. The core
methods in those important and much-used classes were somewhat inefficient.

___JmolVersion="14.3.7_2014.08.25"

bug fix: translation of atoms after deleting atoms having dots on crashes
Jmol

I hope to synchronize this with 14.2 later this week.

Bob

-- 
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] JspecView file path

[Robert Hanson]

I think it is something with the format of those files, nothing more.

Check the console. You have disabled the console on that page by using

Info.console = "consolediv" and then not providing that. So first remove
that assignment and then, after the problem, from the developer console
issue:

jsv._showInfo(true)


and see what it says there.



On Mon, Aug 25, 2014 at 1:54 PM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:

>  I am trying to figure out why we have no trouble with current files in
> the in the Spectral Zoo (http://chemserv.centre.edu/listing3.php?cat=nmr)
> but we cannot see “archived files” that are nested in a folder.  I suspect
> it has to do with the file paths.  The error we see says
> “java.lang.NumberFortmatException:  Not a Number: —“  That’s confusing to
> me, since we are using JSmol and the JS version of JSpecView.  But maybe
> that message has significance to others.
>
>  I welcome any suggestions about how to modify things so that we can see
> files buried in folders.  It gets cumbersome for all of the files to be in
> the main folder.
> Jennifer
>
>
>
>
>
>   Jennifer Muzyka
> 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
>
>
>
>
>
>
>
> --
> Slashdot TV.
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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] A freeze-up scenario

[Robert Hanson]

indeed it does! I will get a corrected version up at chemapps tonight.


On Mon, Aug 25, 2014 at 11:59 AM, Ron Mignery  wrote:

> The following script causes the Jmol application to freeze after the
> translate command.  This does not happen if the dots on command is
> commented out.
> zap
> print _version
> set appendNew false
> x1 ="data \"append a\"\nATOM  1  N   GLY A   1   0.000   0.000
> 0.000\nend \"append a\""
> x2 ="data \"append a\"\nATOM  2  CA  GLY A   1   0.200   1.174
> 0.911\nend \"append a\""
> x3 ="data \"append a\"\nATOM  3  C   GLY A   1  -1.110   1.668
> 1.425\nend \"append a\""
> x4 ="data \"append a\"\nATOM  4  O   GLY A   1  -1.320   1.693
> 2.620\nend \"append a\""
> script inline @x1
> script inline @x2
> script inline @x3
> script inline @x4
> connect
> cpk 100
> dots on
> delete @2
> script inline @x2
> connect
> cpk 100
> select @2
> print "before"
> translate selected {1 1 1}
> print "after"
>
> Results:
> 1402004
> appendNew = false
> 1 atoms deleted
> 1 atoms selected
> before[application is now irrecoverably frozen]
>
>
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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] JspecView file path

[Otis Rothenberger]

Hi Jennifer,

This is just a wild guess, but you have spaces in some folder names that 
are being URL encoded to +. That could be messing up attempts to 
interpret the query string. The error suggests that something in your 
code expects a number. The + could be forcing that issue.


Otis


Jennifer L. Muzyka 
August 25, 2014 at 2:54 PM
I am trying to figure out why we have no trouble with current files in 
the in the Spectral Zoo 
(http://chemserv.centre.edu/listing3.php?cat=nmr) but we cannot see 
“archived files” that are nested in a folder.  I suspect it has to do 
with the file paths.  The error we see says 
“java.lang.NumberFortmatException:  Not a Number: —“  That’s confusing 
to me, since we are using JSmol and the JS version of JSpecView.  But 
maybe that message has significance to others.


I welcome any suggestions about how to modify things so that we can 
see files buried in folders.  It gets cumbersome for all of the files 
to be in the main folder.

Jennifer





Jennifer Muzyka
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





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--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com

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[Jmol-users] JspecView file path

[Jennifer L. Muzyka]

I am trying to figure out why we have no trouble with current files in the in 
the Spectral Zoo (http://chemserv.centre.edu/listing3.php?cat=nmr) but we 
cannot see “archived files” that are nested in a folder.  I suspect it has to 
do with the file paths.  The error we see says 
“java.lang.NumberFortmatException:  Not a Number: —“  That’s confusing to me, 
since we are using JSmol and the JS version of JSpecView.  But maybe that 
message has significance to others.

I welcome any suggestions about how to modify things so that we can see files 
buried in folders.  It gets cumbersome for all of the files to be in the main 
folder.
Jennifer





Jennifer Muzyka
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





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[Jmol-users] A freeze-up scenario

[Ron Mignery]

The following script causes the Jmol application to freeze after the
translate command.  This does not happen if the dots on command is
commented out.
zap
print _version
set appendNew false
x1 ="data \"append a\"\nATOM  1  N   GLY A   1   0.000   0.000
0.000\nend \"append a\""
x2 ="data \"append a\"\nATOM  2  CA  GLY A   1   0.200   1.174
0.911\nend \"append a\""
x3 ="data \"append a\"\nATOM  3  C   GLY A   1  -1.110   1.668
1.425\nend \"append a\""
x4 ="data \"append a\"\nATOM  4  O   GLY A   1  -1.320   1.693
2.620\nend \"append a\""
script inline @x1
script inline @x2
script inline @x3
script inline @x4
connect
cpk 100
dots on
delete @2
script inline @x2
connect
cpk 100
select @2
print "before"
translate selected {1 1 1}
print "after"

Results:
1402004
appendNew = false
1 atoms deleted
1 atoms selected
before[application is now irrecoverably frozen]
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Re: [Jmol-users] Local Storage Revisited

[Rzepa, Henry S]

> On 25 Aug 2014, at 06:55, Otis Rothenberger  wrote:
> 
> This is still pretty rough, but it illustrates the use of local storage for 
> an approach to student class notes:
> 
> http://chemagic.com/JSmolVMK2.htm
> 
> Local storage is being used on two control button screens on this page - Draw 
> and Notes-Misc.
> 
> On the Draw button screen, 10 JSME structures can be saved/retrieved to/from 
> local storage.
> 
> On the Notes-Misc button screen, 10 Jmol models can be saved/retrieved 
> to/from local storage. There is also a text area for student notes. Student 
> notes in this area are auto saved to local storage as they are typed. This 
> screen also has  back-up and erase links for local storage. The back-up link 
> produces cut/paste JSON text that can be used to transfer the data to another 
> browser/computer or simply saved as a text file for data back-up 
> (instructions on Jmol echo window). The erase link erases local storage for 
> this domain. I can envision notes being archived in files according to topic 
> and being loaded as needed.
> 
> Like I mentioned before, this storage is analogous to cookies, but the 
> storage limit is about 5Mb. Ten cholesterol models, ten cholesterol 
> structures, and pages of blah blah blah notes took up a trivial amount of 
> total space allowed.
>   
> The data is persistent until erased or replaced. The auto saved notes reload 
> when the page is opened in the browser of the original save or when a back-up 
> JSON is loaded into a new browser.
> 
> There is some error checking, but I still have a lot of work to do on this. 
> The code for working with local storage is amazingly simple to use. I'm 
> interested in any feedback on how various browsers and platforms respond to 
> all of this.
> 
> Otis
> 


I fully support this very exciting possibility.  Otis and  I discussed the 
potential of eg annotating with a web browser aka https://www.diigo.com/ some 
months back, but for many reasons this approach seems so much better than 
either  Diigo or  Cookies
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