Re: [Jmol-users] isosurfaceData as JVXL string

2013-12-30 Thread Jaime Prilusky
Thank you. This works perfect.
Jaim

On Dec 29, 2013, at 9:47 PM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

Have a desired isosurface as the current isosurface -- if necessary, use

  isosurface ID 

by itself to select.

Then issue:

show isosurface


From JavaScript, you could use:

var xmlData = Jmol.evaluate(jmolApplet0, script('show isosurface'))




On Sat, Dec 28, 2013 at 1:31 PM, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
What's the correct syntax to get from JSmol applet the isosurface data as JVXL 
string in javascript?

I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, 
isosurfaceData) could do.

Thank you in advance,

Happy Holidays,
Jaim




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Re: [Jmol-users] Will unsigned applet be blocked soon?

2013-12-30 Thread Rzepa, Henry S

On 29 Dec 2013, at 20:00, Robert Hanson hans...@stolaf.edu wrote:

 I'm guessing  it will be January 14:
 
 https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias
 http://www.oracle.com/technetwork/topics/security/alerts-086861.html
 
 As I understand it, all applets must be updated. signed or not -- all must 
 be signed, and local file reading now requires the JNLP files as well in the 
 directory of the JAR files. (Note that these JNLP files allow the applet to 
 be started outside a browser as well.)

Using  Jmol  14.0.2 (14th December) uploaded to a server,  I can indeed no 
longer get the applet to load (OS X Mavericks/Safari or Firefox). 

Application blocked by security settings”. 

It also  (falsely) tells me that the  Java security settings have prevented 
this application from running. You may change this behaviour in the Java 
control panel”.  Well,  I could not.  This did not happen with eg 13.3.9.

There are four  JNLP files in this build of  Jmol in the  Java directory  
(including eg JmolApplet.jnlp and JmolAppletSigned.jnlp), but their presence 
has not prevented the above message.

Am struggling slightly.  

Could it be that our  Apache server has no  MIMEtype defined for  JNLP?
Or that  OS X Mavericks Java is broken in this regard?
Or that some other configuration which  I  have omitted is needed?

The relevant page is http://www.ch.ic.ac.uk/rzepa/WEO/ja061400a/?JAVA  (which 
is an ancient page from  ~2007 which  I thought  I might try to rescue).


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Re: [Jmol-users] Will unsigned applet be blocked soon?

2013-12-30 Thread Philip Bays
Henry:

I am using the same OS but downloaded last evening’s release of jmol (14.0.3).  
I test using my sites local network server on an iMac, which should behave like 
an outside server.  My test was to access test2.htm in the jsmol directory.  It 
runs fine with HTML5 and the signed applet. But does not do so when simply 
launched as a file.  I did have to change permissions on the jmol directory.

In my java console (security tabmanage certificates, I see the Integrated 
Graphics certificate as trusted  (That has been true since originally specified 
several iterations of jmol ago.

However, when I try your link, I get the same results as you do.

 
On Dec 30, 2013, at 8:25 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:

 
 On 29 Dec 2013, at 20:00, Robert Hanson hans...@stolaf.edu wrote:
 
 I'm guessing  it will be January 14:
 
 https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias
 http://www.oracle.com/technetwork/topics/security/alerts-086861.html
 
 As I understand it, all applets must be updated. signed or not -- all must 
 be signed, and local file reading now requires the JNLP files as well in the 
 directory of the JAR files. (Note that these JNLP files allow the applet to 
 be started outside a browser as well.)
 
 Using  Jmol  14.0.2 (14th December) uploaded to a server,  I can indeed no 
 longer get the applet to load (OS X Mavericks/Safari or Firefox). 
 
 Application blocked by security settings”. 
 
 It also  (falsely) tells me that the  Java security settings have prevented 
 this application from running. You may change this behaviour in the Java 
 control panel”.  Well,  I could not.  This did not happen with eg 13.3.9.
 
 There are four  JNLP files in this build of  Jmol in the  Java directory  
 (including eg JmolApplet.jnlp and JmolAppletSigned.jnlp), but their presence 
 has not prevented the above message.
 
 Am struggling slightly.  
 
 Could it be that our  Apache server has no  MIMEtype defined for  JNLP?
 Or that  OS X Mavericks Java is broken in this regard?
 Or that some other configuration which  I  have omitted is needed?
 
 The relevant page is http://www.ch.ic.ac.uk/rzepa/WEO/ja061400a/?JAVA  (which 
 is an ancient page from  ~2007 which  I thought  I might try to rescue).
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Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



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Re: [Jmol-users] Will unsigned applet be blocked soon?

2013-12-30 Thread Robert Hanson
The JNLP files are just in the directory with the JAR files. No
installation -- just click on one, and the applet should open.


On Mon, Dec 30, 2013 at 12:21 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote:


 On 29 Dec 2013, at 20:00, Robert Hanson hans...@stolaf.edu wrote:

  I'm guessing  it will be January 14:
 
 
 https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias
  http://www.oracle.com/technetwork/topics/security/alerts-086861.html
 
  As I understand it, all applets must be updated. signed or not -- all
 must be signed, and local file reading now requires the JNLP files as well
 in the directory of the JAR files. (Note that these JNLP files allow the
 applet to be started outside a browser as well.)

 Is there a specific set of instructions for acquiring and installing these
  “JNLP” files for  Jmol?   Using this as a search term in  Bob’s
  documentation http://chemapps.stolaf.edu/jmol/docs/?search=JNLP shows no
 hits.
 
  In addition, recent versions of JSmol JavaScript libraries are required,
 and if you are using the older Jmol.js, library that needs to be updated
 (see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol.js).


 http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol.js   states THIS
 LIBRARY IS DEPRECATED STARTING WITH Jmol 13.0.”

  Or you can add this line yourself in the _jmolApplet function:
  params.permissions = (archivePath.indexOf(Signed) = 0 ?
 all-permissions : sandbox);
 
 
  Feels like Y2K all over again!
 





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[Jmol-users] Cross Domain Load

2013-12-30 Thread Otis Rothenberger
Bob,

I could figure this out by trial and error, but you probably know the answer. 
Will JSmol load sdf text files cross domain?

Otis

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Re: [Jmol-users] Cross Domain Load

2013-12-30 Thread Robert Hanson
as long as the server is allowing full access via its headers.


On Mon, Dec 30, 2013 at 11:42 AM, Otis Rothenberger
osrot...@chemagic.comwrote:

 Bob,

 I could figure this out by trial and error, but you probably know the
 answer. Will JSmol load sdf text files cross domain?

 Otis

 --
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 o...@chemagic.com
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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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Re: [Jmol-users] Cross Domain Load and Help Request

2013-12-30 Thread Otis Rothenberger
OK, Thanks. Are the following observations correct?

Resolver does this.

PubChem does this.

RCSB does not do this.

Otis

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On Dec 30, 2013, at 12:45 PM, Robert Hanson hans...@stolaf.edu wrote:

 as long as the server is allowing full access via its headers.
 
 
 On Mon, Dec 30, 2013 at 11:42 AM, Otis Rothenberger osrot...@chemagic.com 
 wrote:
 Bob,
 
 I could figure this out by trial and error, but you probably know the answer. 
 Will JSmol load sdf text files cross domain?
 
 Otis
 

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[Jmol-users] another Mac surprise

2013-12-30 Thread Robert Hanson
It appears that Safari has a very strange feature -- at least on my
machine, everything works fine using http, but with file://, if I download
Jmol, open the zip file, extract the jsmol directory, and start
simple2.htm, and immediately clicking on the Signed link to get the
signed version, the applet fails to load.

However, if I first open the applet in Firefox, then Safari will open it.
If Safari has opened the file, and I change the directory name, then the
next time I try this, Safari will not start the applet. However, if I then
open that local page in Firefox and then try again in Safari, all is good.

What could possibly be going on? I don't know. But the fact that this is a
new problem suggested to me that it's something recent. I remembered that
recently I changed Safari settings to using the applet tag instead of
object. Well, guess what? When I switch back to using the object tag,
everything works normally. No directory problems; no load issues. Go
figure.

For whatever reason, it looks like we cannot use the applet tag in
Safari. I'm sure I had a reason for switching to that, but I can't remember
that.

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] another Mac surprise

2013-12-30 Thread Greg Edwards
Hi Bob,

Wild idea that I haven't really thought through .. rushing beakfast here ..
but your mention of different results from opening files in different
orders with different apps makes me think of Mac OS X file metadata.
Readable and modifiable via xattr. Eg. this is where Mac puts a tag that a
file has been downloaded and not yet opened, and prompts the This file was
downloaded by browser, are you sure you want to open it prompt.

Best and HNY,
GE.



On 31 December 2013 08:27, Robert Hanson hans...@stolaf.edu wrote:

 It appears that Safari has a very strange feature -- at least on my
 machine, everything works fine using http, but with file://, if I download
 Jmol, open the zip file, extract the jsmol directory, and start
 simple2.htm, and immediately clicking on the Signed link to get the
 signed version, the applet fails to load.

 However, if I first open the applet in Firefox, then Safari will open it.
 If Safari has opened the file, and I change the directory name, then the
 next time I try this, Safari will not start the applet. However, if I then
 open that local page in Firefox and then try again in Safari, all is good.

 What could possibly be going on? I don't know. But the fact that this is a
 new problem suggested to me that it's something recent. I remembered that
 recently I changed Safari settings to using the applet tag instead of
 object. Well, guess what? When I switch back to using the object tag,
 everything works normally. No directory problems; no load issues. Go
 figure.

 For whatever reason, it looks like we cannot use the applet tag in
 Safari. I'm sure I had a reason for switching to that, but I can't remember
 that.

 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] another Mac surprise

2013-12-30 Thread Otis Rothenberger
Safari and Firefox sharing the same Java cache???

This doesn't explain the object vs applet thing, however.

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




On Dec 30, 2013, at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote:

 It appears that Safari has a very strange feature -- at least on my 
 machine, everything works fine using http, but with file://, if I download 
 Jmol, open the zip file, extract the jsmol directory, and start simple2.htm, 
 and immediately clicking on the Signed link to get the signed version, the 
 applet fails to load. 
 
 However, if I first open the applet in Firefox, then Safari will open it. 
 If Safari has opened the file, and I change the directory name, then the next 
 time I try this, Safari will not start the applet. However, if I then open 
 that local page in Firefox and then try again in Safari, all is good. 
 
 What could possibly be going on? I don't know. But the fact that this is a 
 new problem suggested to me that it's something recent. I remembered that 
 recently I changed Safari settings to using the applet tag instead of 
 object. Well, guess what? When I switch back to using the object tag, 
 everything works normally. No directory problems; no load issues. Go figure. 
 
 For whatever reason, it looks like we cannot use the applet tag in Safari. 
 I'm sure I had a reason for switching to that, but I can't remember that.
 
 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] another Mac surprise

2013-12-30 Thread J. Philip Bays
I would think that they both rely on the java console.  I wonder what is
going on with that?


On Mon, Dec 30, 2013 at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote:

 It appears that Safari has a very strange feature -- at least on my
 machine, everything works fine using http, but with file://, if I download
 Jmol, open the zip file, extract the jsmol directory, and start
 simple2.htm, and immediately clicking on the Signed link to get the
 signed version, the applet fails to load.

 However, if I first open the applet in Firefox, then Safari will open it.
 If Safari has opened the file, and I change the directory name, then the
 next time I try this, Safari will not start the applet. However, if I then
 open that local page in Firefox and then try again in Safari, all is good.

 What could possibly be going on? I don't know. But the fact that this is a
 new problem suggested to me that it's something recent. I remembered that
 recently I changed Safari settings to using the applet tag instead of
 object. Well, guess what? When I switch back to using the object tag,
 everything works normally. No directory problems; no load issues. Go
 figure.

 For whatever reason, it looks like we cannot use the applet tag in
 Safari. I'm sure I had a reason for switching to that, but I can't remember
 that.

 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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Notre Dame, IN 46556
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Re: [Jmol-users] another Mac surprise

2013-12-30 Thread Otis Rothenberger
Phil,

Exactly. That's what I'm thinking. Safari won't cache it, but it will pull it 
from cache.

Otis
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On Dec 30, 2013, at 7:28 PM, J. Philip Bays pb...@saintmarys.edu wrote:

 I would think that they both rely on the java console.  I wonder what is 
 going on with that?
 
 
 On Mon, Dec 30, 2013 at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote:
 It appears that Safari has a very strange feature -- at least on my 
 machine, everything works fine using http, but with file://, if I download 
 Jmol, open the zip file, extract the jsmol directory, and start simple2.htm, 
 and immediately clicking on the Signed link to get the signed version, the 
 applet fails to load. 
 
 However, if I first open the applet in Firefox, then Safari will open it. 
 If Safari has opened the file, and I change the directory name, then the next 
 time I try this, Safari will not start the applet. However, if I then open 
 that local page in Firefox and then try again in Safari, all is good. 
 
 What could possibly be going on? I don't know. But the fact that this is a 
 new problem suggested to me that it's something recent. I remembered that 
 recently I changed Safari settings to using the applet tag instead of 
 object. Well, guess what? When I switch back to using the object tag, 
 everything works normally. No directory problems; no load issues. Go figure. 
 
 For whatever reason, it looks like we cannot use the applet tag in Safari. 
 I'm sure I had a reason for switching to that, but I can't remember that.
 
 Bob
 
 
 

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Re: [Jmol-users] another Mac surprise

2013-12-30 Thread Philip Bays
I was having a problem this afternoon with some debugging.  I typically disable 
cache in the developer menu, and use private browsing.   nevertheless, I would 
make a change in my code and the change was not reflected in the browser 
reload.  In fact, I had a line that called on a nonexistent function.  I 
deleted the line, but it kept appearing in the error messages.  Somehow, Safari 
was caching when it was not supposed to be.  I did not have time to explore it 
further, but will tomorrow and see if I can reproduce it.  I did not try 
loading with Firefox and then again with Safari.


On Dec 30, 2013, at 7:48 PM, Otis Rothenberger osrot...@chemagic.com wrote:

 Phil,
 
 Exactly. That's what I'm thinking. Safari won't cache it, but it will pull it 
 from cache.
 
 Otis
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Dec 30, 2013, at 7:28 PM, J. Philip Bays pb...@saintmarys.edu wrote:
 
 I would think that they both rely on the java console.  I wonder what is 
 going on with that?
 
 
 On Mon, Dec 30, 2013 at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote:
 It appears that Safari has a very strange feature -- at least on my 
 machine, everything works fine using http, but with file://, if I download 
 Jmol, open the zip file, extract the jsmol directory, and start simple2.htm, 
 and immediately clicking on the Signed link to get the signed version, the 
 applet fails to load. 
 
 However, if I first open the applet in Firefox, then Safari will open it. 
 If Safari has opened the file, and I change the directory name, then the 
 next time I try this, Safari will not start the applet. However, if I then 
 open that local page in Firefox and then try again in Safari, all is good. 
 
 What could possibly be going on? I don't know. But the fact that this is a 
 new problem suggested to me that it's something recent. I remembered that 
 recently I changed Safari settings to using the applet tag instead of 
 object. Well, guess what? When I switch back to using the object tag, 
 everything works normally. No directory problems; no load issues. Go figure. 
 
 For whatever reason, it looks like we cannot use the applet tag in Safari. 
 I'm sure I had a reason for switching to that, but I can't remember that.
 
 Bob
 
 
 
 
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 Rapidly troubleshoot problems before they affect your business. Most IT 
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu


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