Re: [Jmol-users] Local Storage Revisited
On 25 Aug 2014, at 06:55, Otis Rothenberger osrot...@chemagic.com 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] A freeze-up scenario
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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[Jmol-users] JspecView file path
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.edumailto:jennifer.muz...@centre.edu http://web.centre.edu/muzyka http://organicers.org 859-238-5413 fax 859-236-7925 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JspecView file path
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 mailto:jennifer.muz...@centre.edu 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 mailto:jennifer.muz...@centre.edu http://web.centre.edu/muzyka http://organicers.org 859-238-5413 fax 859-236-7925 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] A freeze-up scenario
indeed it does! I will get a corrected version up at chemapps tonight.
On Mon, Aug 25, 2014 at 11:59 AM, Ron Mignery remign...@gmail.com 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
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. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmol-14.3.7_2014.08.25.zip
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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
