Re: [Jmol-users] Jmol SMILES Question

[Otis Rothenberger]

Excellent! I should have checked the docs.

I have been using an incredibly clumsy way of doing this with Jmol/JSME, and it 
breaks on substituted allenes in JSME.

Otis

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

> On Jun 9, 2017, at 12:09 AM, Robert Hanson  wrote:
> 
> print {*}.find("smiles/nostereo")
> 
> see https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0160-4
> 
> Directives /noStereo/ and /invertStereo/ are very useful because they allow 
> re-use of SMILES strings for different types of stereochemical matches 
> without having to remove or switch the stereochemical designations in the 
> strings themselves, which can be quite complicated. The directive /noStereo/ 
> simply ignores all stereochemistry indicated in the SMILES string, including 
> both stereochemistry at chirality centers as well as cis/trans double-bond 
> stereochemistry. The directive /invertStereo/ inverts all chirality 
> designations, allowing efficient checking for enantiomers. 
> 
> Bob
> 
>> On Thu, Jun 8, 2017 at 3:41 PM, Otis Rothenberger  
>> wrote:
>> Bob,
>> 
>> Can Jmol generate a non-stereo SMILES for a chiral model in the window?
>> 
>> Otis
>> 
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>> 
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
> 
> 
> 
> -- 
> Robert M. Hanson
> 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
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol SMILES Question

[Robert Hanson]

*print {*}.find("smiles/nostereo")*
see https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0160-4


*Directives /noStereo/ and /invertStereo/ are very useful because they
allow re-use of SMILES strings for different types of stereochemical
matches without having to remove or switch the stereochemical designations
in the strings themselves, which can be quite complicated. The directive
/noStereo/ simply ignores all stereochemistry indicated in the SMILES
string, including both stereochemistry at chirality centers as well as
cis/trans double-bond stereochemistry. The directive /invertStereo/ inverts
all chirality designations, allowing efficient checking for enantiomers. *
Bob

On Thu, Jun 8, 2017 at 3:41 PM, Otis Rothenberger 
wrote:

> Bob,
>
> Can Jmol generate a non-stereo SMILES for a chiral model in the window?
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol Anniversaries?

[Paul PILLOT]

Hi,
digging in sourceforge jmol-developers list, I found that Bob starts appearing 
as a recurring character in 2005 and secures the leading role in developping 
Jmol in mid 2006 after having exhausted Miguel with thousands of messages and 
commits. That was around Jmol v10.x
It looks like we missed the 10th anniversary celebration ;)
As for Jsmol, there was an article published in 2013 announcing its release 
(was issued some month after the initial Jsmol tour de force) : 
https://chemapps.stolaf.edu/jmol/2013_Hanson_Prilusky_IJC.pdf 


Paul

> Le 08-06-2017 à 11:09, Eric Martz  a écrit :
> 
> Hi Henry,
> I have a paragraph of Jmol history in footnote 1 here:
> 
> http://proteopedia.org/w/Jmol 
> Which leads to early history by searching for "jmol" at openscience.org:
> http://openscience.org/?s=jmol 
> Much of Jmol's command language was invented by Roger Sayle when he created 
> RasMol. Tim Maffet used Roger's public domain source code when he created the 
> browser plug-in MDL Chime, which was the best within-browser solution from 
> 1996 until Jmol superceded it ca. 2006. Thus, Chime included most of RasMol's 
> command language. Michael "Miguel" Howard, who I believe first adapted Jmol 
> to display macromolecules, incorporated the RasMol/Chime command language 
> into Jmol, facilitating the transitions of RasMol and Chime users to Jmol. Of 
> course Jmol's command language is now vastly larger and more powerful and 
> complex than the languages of RasMol & Chime. But the original RasMol 
> language is still a core subset.
> Although far from complete, quite a bit of pre-Jmol history is here, 
> including physical models and early computer graphics:
> 
> http://History.MolviZ.Org 
> -Eric
> On 6/7/17 2:28 AM, Rzepa, Henry S wrote:
>> Does anyone know the various anniversary dates?
>> 
>> 1. Jmol (was it really only released in 2001?  I thought it came about just 
>> a year or so after  Java itself was released in 1996?)
>> 2. JSmol (2014?)
>> 3. Bob’s own entry after Miguel handed on (??)
>> 
>> Is there a hall of fame, going back perchance to  Xmol (which started the 
>> bandwagon, + Rasmol as a separate fork?) and key timelines/contributors? The 
>> Jmol Wikipedia page is not that strong on the history).
>> 
>> Henry Rzepa, http://orcid.org/-0002-8635-8390 
>> 
>> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! 
> http://sdm.link/slashdot___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Jmol SMILES Question

[Otis Rothenberger]

Bob,

Can Jmol generate a non-stereo SMILES for a chiral model in the window?

Otis


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

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol 14.18.1

[Robert Hanson]

I confirm that Jmol.jar is broken for generation of Cahn-Ingold-Prelog
stereochemical descriptors in Java; the JavaScript should be OK.

On Thu, Jun 8, 2017 at 12:55 PM, Robert Hanson  wrote:

> OK, it could be that I messed up with the distribution. That can happen if
> I forget to do a thorough cleaning of the directories, which is the case
> this time.
> ​
> Bob
>
>


-- 
Robert M. Hanson
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol 14.18.1

[Robert Hanson]

OK, it could be that I messed up with the distribution. That can happen if
I forget to do a thorough cleaning of the directories, which is the case
this time.
​
Bob
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

On Thu, Jun 8, 2017 at 10:58 AM, Rolf Huehne 
wrote:

> Am 08.06.17 um 14:41 schrieb Robert Hanson:
>
>> RIP,  Java applets.
>>
>> Since there still are many situations where the superior Java performance
> would be helpful (large structures; surfaces; complex Jmol scripts that are
> running about 50 times slower in the Javascript version) it would still be
> good to have a Java version with the flexibility of the applet to build
> customized user interfaces.
>
> sorry, didn't mean to imply that we were dropping applet production.  It's
all produced in a few clicks of a button -- Jmol app, Jmol applet,
JmolData, JSmol. So I will keep that happening the same.



> I am wondering how much effort it would be to extend the applet by a
> HTML/CSS rendering and Javascript engine like it is provided by systems
> like 'JavaFX - WebView Component (https://docs.oracle.com/javas
> e/8/javafx/api/toc.htm https://stackoverflow.com/ques
> tions/2438201/pure-java-html-viewer-renderer-for-use-in-a-scrollable-pane),
> Oracle Nashorn (http://www.oracle.com/technetwork/articles/java/jf14-
> nashorn-2126515.html), and HtmlUnit (http://htmlunit.sourceforge.net/).
>
> I woud guess one of the critical points would be how much of the
> Javascript/Applet communication would still be possible in such application.
>

I don't know anything about JavaFX, but it's not clear to me there has been
any development on it since 2012 or 2014. Maybe just an idea that never
took off? Do you see some advantage to this?

Bob
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Fwd: Jmol-users Digest, Vol 133, Issue 3

[Craig T Martin]

Henry

   I just checked the most recent Safari Developer Preview (32), running under 
Sierra.
Release 32 (Safari 11.0, WebKit 12604.1.23.0.4)

   Java is supported. I’ve sent you two screenshots showing this.

   I provide this only for clarity. I share your concern that Apple may very 
well ban Java in the near future. And with good reason...

Best regards

Craig

PS - I am very impressed by JSMol on my Mac - I have a very large and complex 
protein and it zips along! So as soon as I catch up on porting things to JSmol, 
I’ll be happy to see Java support go away.

  (sadly, JSmol is not so fast on my iPad Pro…)

> Begin forwarded message:
> 
> From: jmol-users-requ...@lists.sourceforge.net 
> 
> Subject: Jmol-users Digest, Vol 133, Issue 3
> Date: June 8, 2017 at 8:18:53 AM EDT
> To: jmol-users@lists.sourceforge.net 
> Reply-To: jmol-users@lists.sourceforge.net 
> 
> 
> Message: 5
> Date: Thu, 8 Jun 2017 10:29:56 +
> From: "Rzepa, Henry S"  >
> To: " >"
>    >
> Cc: "Rzepa, Henry S" >
> Subject: [Jmol-users] Java will go from Safari as well as already gone
>   from Opera, FF and Chrome
> Message-ID:  >
> Content-Type: text/plain; charset="utf-8"
> 
> I have had a look at Safari preview 32.  In the preferences/security tab, the 
> current production safari has settings for
> 
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow  
> Java.
> 
> In Safari 32, both of these are now gone.   With  High Sierra developer 
> preview about to be released into  beta, may bring confirmation that  Safari 
> too has now not merely been deprecated but disallowed. 
> 
> If correct, this means that Jmol.jar can only now run in application mode, 
> and not as a browser plugin. 
> 
> Still,  Apple promise that the new Safari will be  ?faster?, although  I 
> suspect it has some way to go to be as fast as compiled Java. 
> 
> 
> I wonder what the missing  WebGL means? It never really took off did it!
> 
> Henry
> -- next part --
> A non-text attachment was scrubbed...
> Name: smime.p7s
> Type: application/pkcs7-signature
> Size: 2682 bytes
> Desc: not available

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rolf Huehne]

Am 08.06.17 um 14:41 schrieb Robert Hanson:

RIP,  Java applets.

Since there still are many situations where the superior Java 
performance would be helpful (large structures; surfaces; complex Jmol 
scripts that are running about 50 times slower in the Javascript 
version) it would still be good to have a Java version with the 
flexibility of the applet to build customized user interfaces.


I am wondering how much effort it would be to extend the applet by a 
HTML/CSS rendering and Javascript engine like it is provided by systems 
like 'JavaFX - WebView Component 
(https://docs.oracle.com/javase/8/javafx/api/toc.htm 
https://stackoverflow.com/questions/2438201/pure-java-html-viewer-renderer-for-use-in-a-scrollable-pane), 
Oracle Nashorn 
(http://www.oracle.com/technetwork/articles/java/jf14-nashorn-2126515.html), 
and HtmlUnit (http://htmlunit.sourceforge.net/).


I woud guess one of the critical points would be how much of the 
Javascript/Applet communication would still be possible in such application.


Regards,
Rolf

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol 14.18.1

[Bruce Tattershall]

Bob

I have emptied both the Java cache in my PC and the browser cache (IE11 with 
java plugin), and get
exactly the same behaviour from the Jmol_S applet.   I get the same error 
message if I try
label %[cipRule]
and no labels are produced.Normal default atom labelling works as usual, so 
the error seems to be in the
chirality stuff.

If I use the JSmol applet, I get a different behaviour in IE11.   I get a 
message box saying
RangeError: Argument list too large to apply
This message comes up twice.   After OKing it for the second time, the 
chirality labels appear only on the
rule 1a atoms.

A following
label %[cipRule]
command then works straightaway, but still labels only the rule 1a atoms.

If, after refresh, I give the two commands in the opposite order, I still get 
the two error messages on the
first command, and no error messages on the second.   The labelling each does 
is the same for each,
whatever the order.

JSmol in Firefox in the PC gives a bit more explicit error message:
RangeError:  arguments array passed to Function.prototype.apply is too large
Otherwise its behaviour is the same as in IE11.

Jmol_S in Firefox with Java plugin fails in the same way as IE11 with Java, 
either using
Firefox in the PC or Firefox in Linux.

JSMol in Firefox in Linux works fine, as does JSMol in Chrome in the PC.
I guess that you may have used one of these for your tests.

As for Jmol.jar as an application in Linux, I was able to get some more 
information from the
Java Jmol Console.
It seems to show that the cache had been emptied, twice, and that loading of 
the model was normal.
When I gave the
label %[chirality]
command, the Java Jmol Console then showed a considerably more explicit error 
message series, which
I send as a DOS text attachment.
As I said yesterday, no labels were produced.

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 08 June 2017 04:35
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.18.1

You will have to clear your cache.

On Wed, Jun 7, 2017 at 11:43 AM, Bruce Tattershall 
> 
wrote:
Sorry Bob, but this version fails to do any chirality labelling for me, for 
either of my two models which you
looked at yesterday.
The following is copied from the Jmol Script Console:

label %[chirality]

script ERROR: java.lang.AbstractMethodError: 
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge; 
org.jmol.shape.Labels set label

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 07 June 2017 14:15
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol 14.18.1

Jmol.___JmolVersion="14.18.1"  // 2017.06.06

Jmol-14.18.1-binary.zip (69.8 
MB)

new feature: WRITE SDF writes > < user data
 -- can be set using   MODEL PROPERTY "molData" x  where x is an associative 
array
 -- can be read using _M.molData

new feature: associativeArray.pop() -- clears associativeArray

new feature: assArray1.push(assArray2) -- adds all key/value entries in 
assArray2 to assArray1.

new feature: assArray1 + assArray2  -- adds all key/value entries into a new 
associative array. (Complements a1 - a2)

bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
 -- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
 -- see AY236.179 (3D structure was diasteriomer, so I missed that)

bug fix: WRITE MOL should not generate >  because it is  
not SDF format
bug fix: WRITE SDF should generate >  with a trailing 
space

bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for 
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4





--
Robert M. Hanson
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

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users



--
Robert M. Hanson
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
vwr handling error condition: java.lang.AbstractMethodError: 
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge;  
java.lang.AbstractMethodError: 

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Eric Martz]

Hi, Henry,

In addition to Internet Explorer 11* (still included in Windows 10 as 
far as I know), several minor browsers that still supported Java when 
last I checked in March 2017 are listed here:


http://proteopedia.org/w/Installing_and_enabling_Java#Browsers_That_Support_Java

* See

http://proteopedia.org/w/Installing_and_enabling_Java#Accessing_Internet_Explorer_in_Windows_10

-Eric

On 6/8/17 6:29 AM, Rzepa, Henry S wrote:

I have had a look at Safari preview 32.  In the preferences/security tab, the 
current production safari has settings for

1. Allow WebGL
2. Allow Internet Plugins,  and in this latter one can configure to allow  Java.

In Safari 32, both of these are now gone.   With  High Sierra developer preview 
about to be released into  beta, may bring confirmation that  Safari too has 
now not merely been deprecated but disallowed.

If correct, this means that Jmol.jar can only now run in application mode, and 
not as a browser plugin.

Still,  Apple promise that the new Safari will be  “faster”, although  I 
suspect it has some way to go to be as fast as compiled Java.


I wonder what the missing  WebGL means? It never really took off did it!

Henry


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol Anniversaries?

[Eric Martz]

Hi Henry,

I have a paragraph of Jmol history in footnote 1 here:

http://proteopedia.org/w/Jmol

Which leads to early history by searching for "jmol" at openscience.org:

http://openscience.org/?s=jmol

Much of Jmol's command language was invented by Roger Sayle when he 
created RasMol. Tim Maffet used Roger's public domain source code when 
he created the browser plug-in MDL Chime, which was the best 
within-browser solution from 1996 until Jmol superceded it ca. 2006. 
Thus, Chime included most of RasMol's command language. Michael "Miguel" 
Howard, who I believe first adapted Jmol to display macromolecules, 
incorporated the RasMol/Chime command language into Jmol, facilitating 
the transitions of RasMol and Chime users to Jmol. Of course Jmol's 
command language is now vastly larger and more powerful and complex than 
the languages of RasMol & Chime. But the original RasMol language is 
still a core subset.


Although far from complete, quite a bit of pre-Jmol history is here, 
including physical models and early computer graphics:


http://History.MolviZ.Org

-Eric

On 6/7/17 2:28 AM, Rzepa, Henry S wrote:

Does anyone know the various anniversary dates?

1. Jmol (was it really only released in 2001?  I thought it came about 
just a year or so after  Java itself was released in 1996?)

2. JSmol (2014?)
3. Bob’s own entry after Miguel handed on (??)

Is there a hall of fame, going back perchance to  Xmol (which started 
the bandwagon, + Rasmol as a separate fork?) and key 
timelines/contributors? The Jmol Wikipedia page is not that strong on 
the history).


Henry Rzepa, http://orcid.org/-0002-8635-8390

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

09/29/2005  08:18 AM 1,813,012 ch3cl-density.cub
09/17/2006  07:47 AM   600,830 ch3cl-density.cub.gz
06/08/2017  08:39 AM 4,631 ch3cl-density.jvxl
06/08/2017  08:40 AM 2,928 ch3cl-density.jvxl.gz

So that is 390:1 with just the JVXL, or 619:1 compression using JVXL+GZ.

(There is never a need to use GZ for web-based files; they almost certainly
will be automatically gzipped by the server anyway.)

So I can't say I'm super impressed. If it's truly full volume data, that
would be impressive.

Bob


On Thu, Jun 8, 2017 at 7:48 AM, Rzepa, Henry S 
wrote:

>
> > On 8 Jun 2017, at 13:45, Robert Hanson  wrote:
> >
> > ps -- neither of the VMD images at http://www.ch.imperial.ac.uk/
> rzepa/blog/?p=18365#comment-243964 are volume rendering, by the way. They
> are just surfaces, one with reflection; one just a mesh. Right?
>
> Yes.  The  reduction in cube size of  ~500 is impressive, but then  JVXL
> manages ~100 (and perhaps more if compressed?)
>
> Contact  Brian Skinner for the inside story.  bsk...@alum.mit.edu
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rzepa, Henry S]

> On 8 Jun 2017, at 13:45, Robert Hanson  wrote:
> 
> ps -- neither of the VMD images at 
> http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 are volume 
> rendering, by the way. They are just surfaces, one with reflection; one just 
> a mesh. Right?

Yes.  The  reduction in cube size of  ~500 is impressive, but then  JVXL 
manages ~100 (and perhaps more if compressed?)

Contact  Brian Skinner for the inside story.  bsk...@alum.mit.edu

> 
> On Thu, Jun 8, 2017 at 7:41 AM, Robert Hanson  wrote:
> RIP,  Java applets.
> 
> On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S  wrote:
> I have had a look at Safari preview 32.  In the preferences/security tab, the 
> current production safari has settings for
> 
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow  
> Java.
> 
> In Safari 32, both of these are now gone.   With  High Sierra developer 
> preview about to be released into  beta, may bring confirmation that  Safari 
> too has now not merely been deprecated but disallowed.
> 
> If correct, this means that Jmol.jar can only now run in application mode, 
> and not as a browser plugin.
> 
> Still,  Apple promise that the new Safari will be  “faster”, although  I 
> suspect it has some way to go to be as fast as compiled Java.
> 
> 
> I wonder what the missing  WebGL means? It never really took off did it!
> 
> ?? WebGL is fantastic. Everyone is using it, including JSmol if you use that 
> option. See this note relative to WebGPU, though: 
> https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/
> 
> Is curious, though. I can't seem to find any reference to WebGL at the 
> preview site. Where do you see that, Henry?
> 
> 
> Bob
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> 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
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! 
> http://sdm.link/slashdot___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users



smime.p7s
Description: S/MIME cryptographic signature
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

ps -- neither of the VMD images at
http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 are volume
rendering, by the way. They are just surfaces, one with reflection; one
just a mesh. Right?

On Thu, Jun 8, 2017 at 7:41 AM, Robert Hanson  wrote:

> RIP,  Java applets.
>
> On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S 
> wrote:
>
>> I have had a look at Safari preview 32.  In the preferences/security tab,
>> the current production safari has settings for
>>
>> 1. Allow WebGL
>> 2. Allow Internet Plugins,  and in this latter one can configure to
>> allow  Java.
>>
>> In Safari 32, both of these are now gone.   With  High Sierra developer
>> preview about to be released into  beta, may bring confirmation that
>> Safari too has now not merely been deprecated but disallowed.
>>
>> If correct, this means that Jmol.jar can only now run in application
>> mode, and not as a browser plugin.
>>
>> Still,  Apple promise that the new Safari will be  “faster”, although  I
>> suspect it has some way to go to be as fast as compiled Java.
>>
>>
>> I wonder what the missing  WebGL means? It never really took off did it!
>>
>
> ?? WebGL is fantastic. Everyone is using it, including JSmol if you use
> that option. See this note relative to WebGPU, though:
> https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/
>
> Is curious, though. I can't seem to find any reference to WebGL at the
> preview site. Where do you see that, Henry?
>
>
> Bob
>
>


-- 
Robert M. Hanson
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

RIP,  Java applets.

On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S 
wrote:

> I have had a look at Safari preview 32.  In the preferences/security tab,
> the current production safari has settings for
>
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow
> Java.
>
> In Safari 32, both of these are now gone.   With  High Sierra developer
> preview about to be released into  beta, may bring confirmation that
> Safari too has now not merely been deprecated but disallowed.
>
> If correct, this means that Jmol.jar can only now run in application mode,
> and not as a browser plugin.
>
> Still,  Apple promise that the new Safari will be  “faster”, although  I
> suspect it has some way to go to be as fast as compiled Java.
>
>
> I wonder what the missing  WebGL means? It never really took off did it!
>

?? WebGL is fantastic. Everyone is using it, including JSmol if you use
that option. See this note relative to WebGPU, though:
https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/

Is curious, though. I can't seem to find any reference to WebGL at the
preview site. Where do you see that, Henry?


Bob
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] HDF5 compression for Cube files?

[Robert Hanson]

Henry,

Good to hear from you!

Could be interesting. From my reading, HDF5 just uses standard ZLIB
compression  (ZIP, GZ) [
https://support.hdfgroup.org/HDF5/faq/compression.html]. I suppose there
might be some difference with that and its alternative SZIP, but I don't
find any comparisons for that with a quick search.

>From the blog comment, it looks to me he is talking specifically about
volume rendering, which is not what JVXL is for, and which Jmol is not set
up to do. JVXL is specifically for surface rendering, where it reduces a 3D
data problem to a 1D problem, thus the huge 300+:1 efficiencies relate to
cube files.

Bob




On Thu, Jun 8, 2017 at 12:28 AM, Rzepa, Henry S 
wrote:

> I have used the excellent  JVXL for reducing cube files to a selected
> isosurface.  Brian Skinner
>
> ( http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 ) has
> indicated work he is doing o the  HDF5 format for reducing cube files,
> where he can obtain up to 530 fold reduction in file sizes.
>
> Does anyone know if  HDF5 has been investigated for  JSmol support?
>
>
> Henry Rzepa, http://orcid.org/-0002-8635-8390
>
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Rzepa, Henry S]

I have had a look at Safari preview 32.  In the preferences/security tab, the 
current production safari has settings for

1. Allow WebGL
2. Allow Internet Plugins,  and in this latter one can configure to allow  Java.

In Safari 32, both of these are now gone.   With  High Sierra developer preview 
about to be released into  beta, may bring confirmation that  Safari too has 
now not merely been deprecated but disallowed. 

If correct, this means that Jmol.jar can only now run in application mode, and 
not as a browser plugin. 

Still,  Apple promise that the new Safari will be  “faster”, although  I 
suspect it has some way to go to be as fast as compiled Java. 


I wonder what the missing  WebGL means? It never really took off did it!

Henry

smime.p7s
Description: S/MIME cryptographic signature
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users