from:"Pierluigi Quagliotto"

Dear Bob,

Many thanks for your reply! I will  try immediately and I will let you knows s 
soon as possible.

Yes, I am trying it locally, with Firefox on a CentOS Linux 6.5 driven virtual 
machine, since this is the operating system that is used on my University cloud 
to host small servers, so I had no choice... ;).
Before posting I made several trials and as far as I can remember I also tried 
to use the whole, complete, URL address, but I will try again following your 
advice. I started by inspecting the code of a page of Angel, since this seemed 
performing the visualization I needed to reproduce and  I found that he applied 
the declaration of the Info variable in the head before using the getApplet 
command in the body section. The problem arises in a very simple page where the 
simple JSME and JSMol are introduced, just to let the user to draw a molecule 
and transfer it into JSMol. To inspect the problem nature I eliminated all code 
that was not directly interesting for this basic duty. 

My basic idea was to insert in a mySQL DB  (using MolDB5r from Prof. Harder, 
Wien University, Austria) several molecules with some descriptor, like IUPAC 
name to make available to my students (and external students, when properly 
working and the DB will be sufficiently populated...) some kind of problems to 
make their practice. I tried to use JSMol to help students in the assign 
correctly the chirality and while more or less the code is just the same, apart 
from JSMol part of the code, this should (and really works!) properly.

As a matter of fact, I have already found some difference when using typical 
HTML code introduced in Joomla. As an example, when using a button.. tag 
you will not be able to pass any variable by POST to the same page by reloading 
it... The result is that when one clicks on the button the page is immediately 
reloaded without real interaction with the user request. By using the older 
tag input type=button  things work as one would expect. By this, I 
would imagine that also something in the code of the CMS could also interacting 
with the user introduced code. I would also try different extension of Joomla 
to work directly with code into articles. Maybe this could also be related to 
those extension programming, being not able to parse correctly but I am quite 
sceptic about it. The extensions, normally, work well or do not work at all.

Sorry of the long post When working properly I will be glad to let you and 
the community informed about tips  tricks, skills and so on... ...related to 
the use of JSME and JSMol in a CMS like Joomla and let available the code I 
used (not so great thing, but for newbies it could help to solve problems and 
to get new ideas, like your code helped me).

Many thanks again!

Best regards,

Pierluigi Quagliotto

Inviato da iPad

 Il giorno 14/mar/2014, alle ore 00:01, Robert Hanson hans...@stolaf.edu ha 
 scritto:
 
 Pierluigi,
 
 Welcome! 
 
 That message indicates that your installation is missing critical files. 
 Perhaps they are on a different server; perhaps they were omitted. If your 
 script tag, for example, reads:
 
 script src=http://verdi.unito.it/jsmol/JSmol.min.js;/script
 
 then you need to make sure that the Info array passed in the getApplet 
 command also points that for j2s:
 
 Info = {
   ...
   j2s: http://verdi.unito.it/jsmol/j2s;,
   ...
 }
 
 because the default location for all the system files is ./j2s in the 
 directory of your page. 
 
 That's probably all you need to do. 
 
 A tip: Best to test in Firefox and not MSIE or Chrome first, particularly if 
 you are testing locally (which it does not sound like you are doing).
 
 Bob Hanson
 
 
 
 On Thu, Mar 13, 2014 at 5:00 PM, pierluigi.quaglio...@unito.it wrote:
 Dear Bob and dear all,
 
 I am trying to set-up a server to help my students to learn organic
 chemistry and, due to this, I tried to use a CMS (Joomla, 2.5.17
 version, stable, for long term production). The site should be available
 in a few days, when IT services of my University (University of Torino,
 Italy) will finish some work about hosting it.
 
 I use JSME and JSMOl, at a very basic level... I am a newbie about
 them. However, I prepared some pages starting by looking at the code of
 some JSME/JSMOL examples and they can work fine if used as stand-alone
 pages, i.e also by wrapping them  into an article in Joomla. The
 problem  arises when I try to use this code into a Joomla article.
 Obviously I have to separate code to inject it properly into head
 section and this work fine for JSME, no problem about it. On the
 contrary, JSMOL start its set-up but it stuck leaving those messages:
 
 
 mol._Canvas2D (Jmol) myJSmol[x]
 loading... j2s/core/package.js
 loading... j2s/core/package.js -- required by w3c script failed
 
 It seems that the program can see correctly the location of the
 JSmol.min.js sinc eit starts to initialize itself but something went
 wrong while loading package.js
 Since

Re: [Jmol-users] can JSMOL be used into the Joomla CMS?

Dear Bob,

It Works!

is it quite strange... When I try modifications I 
usually save the code in a file... and I have 
found that I tried already the modification you suggested..

It did not work... but now, by repeating to make the modification... it works!

Probably it was matter of some character left or 
missing... Sorry to have bothered you... 
Programmers, especially when they are newbie as I 
am, should always wear glasses to look well into their own code!

I will try to manage all site pages which are 
powered by JSmol in order to get them working... 
and as soon as possible I hope to have the site 
on-line nd to let you see if this can be useful for the community.

Obviously when the site will be on-line l will 
write down a few lines as a review on sourceforge 
as I anticipated, so, besides the review we will 
get the sourceforge page indexed also with the 
name of Joomla and people searching for both 
Joomla and chemistry will be aware of JSMol!

Many thanks for your kindness and for the help!

Best regards,

Pierluigi Quagliotto

At 00.01 14/03/2014, you wrote:
into the Joomla CMS?

Dr. Pierluigi Quagliotto - Ph.D. in Chemical Sciences
Faculty Researcher
Università degli Studi di Torino
Dipartimento di Chimica
via Pietro Giuria 7, 10125-TORINO - Italy
Tel. 0039-011-6707593
Fax  0039-011-6707591
First Personal Fax: 0039-011-2367593
Second Fax 0039-02-700448783
E-Mail: pierluigi.quaglio...@unito.it
http://www.chimgenorg.unito.it 


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Re: [Jmol-users] R: can JSMOL be used into the Joomla CMS?

Many Thanks to Bob, for the help and to Pino for 
the suggestion! I looked over it already, but CMS 
sometimes request fine tuning of our code, at least apparently

thanks to all of you,

Pieruigi


At 12.49 14/03/2014, you wrote:
Pierluigi, i use JSmol in wordpress 
installation. have a look at wiki of JSmol
for what i wrote for wordpress. It should not be that much different.
Pino

 Messaggio originale
 Da: pierluigi.quaglio...@unito.it
 Data: 13/03/2014 23.00
 A: jmol-users@lists.sourceforge.net
 Ogg: [Jmol-users] can JSMOL be used into the Joomla CMS?
 
 Dear Bob and dear all,
 
 I am trying to set-up a server to help my students to learn organic
 chemistry and, due to this, I tried to use a CMS (Joomla, 2.5.17
 version, stable, for long term production). The site should be available
 in a few days, when IT services of my University (University of Torino,
 Italy) will finish some work about hosting it.
 
 I use JSME and JSMOl, at a very basic level... I am a newbie about
 them. However, I prepared some pages starting by looking at the code of
 some JSME/JSMOL examples and they can work fine if used as stand-alone
 pages, i.e also by wrapping them  into an article in Joomla. The
 problem  arises when I try to use this code into a Joomla article.
 Obviously I have to separate code to inject it properly into head
 section and this work fine for JSME, no problem about it. On the
 contrary, JSMOL start its set-up but it stuck leaving those messages:
 
 
 mol._Canvas2D (Jmol) myJSmol[x]
 loading... j2s/core/package.js
 loading... j2s/core/package.js -- required by w3c script failed
 
 It seems that the program can see correctly the location of the
 JSmol.min.js sinc eit starts to initialize itself but something went
 wrong while loading package.js
 Since the same code works well when used in a stand-alone php file, the
 location of JSMol dir and subdir should be properly recognized.
 
 do you have any suggestion? I can post some code if requested.
 
 Since I have never found in the web something talking about the use of
 JSME/JSMOL into the Joomla CMS, I would take the opportunity of the
 Bob's request for a review into the sourceforge site to write something
 and cite also this opportunitty to use JSMOL into the Joomla CMS
 container, obviously when I will get it working... ;)
 
 Sorry to bother you,
 
 Best regards,
 
 Pierluigi Quagliotto
 

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Università degli Studi di Torino
Dipartimento di Chimica
via Pietro Giuria 7, 10125-TORINO - Italy
Tel. 0039-011-6707593
Fax  0039-011-6707591
First Personal Fax: 0039-011-2367593
Second Fax 0039-02-700448783
E-Mail: pierluigi.quaglio...@unito.it
http://www.chimgenorg.unito.it 


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Re: [Jmol-users] R: can JSMOL be used into the Joomla CMS?

Dear Angel,

many thanks. Once I will have the site on-line 
and well behaving... I will wirte something and I 
will elt you know before posting into the wiki so 
that you can suggest me relevant corrections, if any.

Best regards,

Pierluigi

At 15.53 14/03/2014, you wrote:
Hello Pierluigi

I was about to suggest something, though Pino was quicker.
Any technical information on how to implement J(S)mol into your CMS
will be a welcome contribution in Jmol Wiki

For example, home page, left column in the main panel (about 1 screen
down) has
Jmol Applications
and then
CMS Using Jmol

Please be free and welcome to add your own subsection there for
Joomla



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Università degli Studi di Torino
Dipartimento di Chimica
via Pietro Giuria 7, 10125-TORINO - Italy
Tel. 0039-011-6707593
Fax  0039-011-6707591
First Personal Fax: 0039-011-2367593
Second Fax 0039-02-700448783
E-Mail: pierluigi.quaglio...@unito.it
http://www.chimgenorg.unito.it 


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Re: [Jmol-users] R: can JSMOL be used into the Joomla CMS?

Dear Angel,

That's OK.

We will see what I will be able to obtain...! The local version of the site 
works properly now, with JSMol. I would hope to get my site on-line in a fast 
way, to obtain final considerations and to let  you see the final results. The 
use of JSME and JSMol in this site is more or less similar to pages that your 
group prepared. Your code inspired me by seeing how things are working in real 
application. My contribution is on very simple code to make requests to a mySQL 
DB in which I can store molecules to help student to make practice with organic 
nomenclature.

Have a nice weekend!

Pierluigi



Inviato da iPad

Il giorno 14/mar/2014, alle ore 20:00, Angel Herráez angel.herr...@uah.es ha 
scritto:

 Pierluigi,
 
 OK, but you can also go ahead and post it -- I will se the changes 
 and we can fine-tune later on the real thing, the Wiki is made that 
 way. No problem for having provisional text.
 
 
 Dear Angel,
 
 many thanks. Once I will have the site on-line 
 and well behaving... I will wirte something and I 
 will elt you know before posting into the wiki so 
 that you can suggest me relevant corrections, if any.
 
 
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Re: [Jmol-users] NMR predictions

2014-04-05 Thread Pierluigi Quagliotto

The same happened to me on iPad first and after on PC and Mac.

Best regards,

Pierluigi Quagliotto


Inviato da iPad

Il giorno 05/apr/2014, alle ore 18:16, Pshemak Maslak n...@psu.edu ha scritto:

 
 http://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm
 http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm
 
 do not work with the newst Jmol version. .  Error message:
 
 JSV.exception.JSVException: Error reading data: 
 java.lang.NullPointerException
 
 Is it Jmol or any of the other servers?
 
 BTW: does the spectra-simulation algorithm takes into account 
 diastereoscopic protons?
 
 
 PM
 
 
 
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Re: [Jmol-users] NMR predictions

2014-04-06 Thread Pierluigi Quagliotto

Bob,

many thanks for your information about the EPFL server failure.

Regards,

Pierluigi Quagliotto

At 22.48 05/04/2014, you wrote:
This indicates a server failure. The direct test 
of that site is 
http://chemapps.stolaf.edu/jmol/jsmol/testEPFL.htmhttp://chemapps.stolaf.edu/jmol/jsmol/testEPFL.htm

Bob





On Sat, Apr 5, 2014 at 12:36 PM, Pierluigi 
Quagliotto 
mailto:pierluigi.quaglio...@unito.itpierluigi.quaglio...@unito.it wrote:
The same happened to me on iPad first and after on PC and Mac.

Best regards,

Pierluigi Quagliotto


Inviato da iPad

Il giorno 05/apr/2014, alle ore 18:16, Pshemak 
Maslak mailto:n...@psu.edun...@psu.edu ha scritto:

 
  
 http://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htmhttp://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm
  http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm
 
  do not work with the newst Jmol version. .  Error message:
 
  JSV.exception.JSVException: Error reading data:
  java.lang.NullPointerException
 
  Is it Jmol or any of the other servers?
 
  BTW: does the spectra-simulation algorithm takes into account
  diastereoscopic protons?
 
 
  PM
 
 
 
  
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Dipartimento di Chimica
via Pietro Giuria 7, 10125-TORINO - Italy
Tel. 0039-011-6707593
Fax  0039-011-6707591
First Personal Fax: 0039-011-2367593
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Re: [Jmol-users] Apology, and request for help

2014-05-16 Thread Pierluigi Quagliotto

Sorry for some unwanted english mistakes, but I am writing  from iPad and the 
automated corrector changed something here and there



Inviato da iPad

Il giorno 16/mag/2014, alle ore 21:34, Pierluigi Quagliotto 
pierluigi.quaglio...@unito.it ha scritto:

 Dear Brenton, and Dear Angel,
 
 The task could not be easy, but also, an answer could be done. At least for 
 the two most important and used Content Managing Systems, also known as CMS, 
 the thing is possible. 
 
 For the easiest CMS to be managed, Wordpress, the most used to host blog 
 sites, please refer to this address:
 
 http://pinostriccoli.altervista.org
 
 The author, Pino Striccoli, used this to give a lot of info and examples to 
 his students. Several pages are a good way to shed light on the way JMol or 
 JSMol can be used into it. 
 
 I am ready to publish a site made with Joomla, the other CMS. This site 
 should have to be ready about two months ago, but unfortunately, the hosting 
 service of my University was rebuilt in those last months, so I am waiting 
 that all the system can work well before activating the site.
 
 So, it is possibile and the real problem is how to solve some problems. As 
 Angel anticipated, in CMS site or blogs, the author and users can normally 
 introduce plain text. Sometimes it is possibile to format the text with some 
 HTML commands, but this is related to a choice of the site Administrator that 
 can activate this option. 
 
 If the blog is your personal blog you should have access to the 
 administrative panel of the blog. 
 
 In this case you should be able to solve our problems even it could seem a 
 bit tricky at a first sight. The page of an article or post is built by the 
 CMS that drive all the process. The text of the post is inserted in a large 
 part of HTML code that the CMS build to let your browser to give the typical 
 graphical aspect of the site. You have to face 2 main problems. To prepare a 
 HTML page  that uses JSMol, you should introduce the declaration of the jsmol 
 file, with javascript. The second one is to make able the CMS to read the 
 post as an HTML code so that it can be introduced by the CMS into the page 
 to be delivered.
 
 Those two problems can be solved since those CMS can be extended in their 
 basic fucntins by using extension that can be modules, components and 
 plugins. Both Joomla and Wordpress have plugins that can help the 
 admiistrator to insert code into the HEAD section, to solve the Javascript 
 declaration and also plugins that can let you inserting HTML code into the 
 post. 
 
 Depending the complexity of the JSMol use into the blog post, you  should 
 become familiar also with javascript and PHP, two programming languages.
 
 you can start to replicate some very basic example pages of JMol eamples by 
 looking into their code and trying to put all things in the right place into 
 the CMS. Only when things will become a bit more complicated, you should 
 acquire javascript and PHP knowledge.
 
 I started in the last days of December and a version of my site was working 
 and  to be published by the end of February, but the problems in the hosting 
 service caused me to delay.
 
 Do not give up... We were all noob at our beginning... The great problem is 
 to have time. 
 
 Just a final note: all what I described is possible if you are the 
 administrator of rhe blog. if you only want to show some JSMol application 
 into a post of an existing blog of which you are not the owner and 
 administrator, it is nearly impossible, because to avoid hacking, the blogs 
 and sites do not permit to introduce code to simpel users.
 
 Good luck!
 
 Pierluigi Quagliotto
 
 
 Inviato da iPad
 
 Il giorno 16/mag/2014, alle ore 15:36, Angel Herráez angel.herr...@uah.es 
 ha scritto:
 
 Brenton,
 
 That's not easy. Not just a question of how to edit html code, but 
 blogs have their underlying engines designed to easy editing TEXT, 
 which make doing advanced under-the-hood things actually more 
 complex.
 
 Have a look at
 
 http://wiki.jmol.org/index.php/Blogs_Using_Jmol
 
 http://wiki.jmol.org/index.php/CMS_Using_Jmol
 
 On the other hand, the HTM files included in J(S)mol download are 
 templates that you could use as code to use and customize, but that's 
 probably not going to work in a blog.
 
 Another choice is using Jmol Export to Web, an utility included in 
 the Jmol application. It will build fpr you web pages with embedded 
 JSmol into them, but probably not working inside a blog.
 
 I'd rather not discourage you, but you may need to abandon your plan. 
 Doing sophisticated things requires time to learn, by practice, trial 
 and error. No quick simple recipe!
 
 Good luck!
 
 
 
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Re: [Jmol-users] support needed -- XHR -- asynchronous vs synchronous

2014-08-31 Thread Pierluigi Quagliotto

Dear Bob,

Would it be opportune and sufficient an intervention by someone like me,
who have not so great programming skills? I could stress the importance of
JMol/JSMol even for simple projects devoted to education and knowledge
spreading in the chemisty and biology fields, not much, probably... ...but
if you think that the users can play a role, it would be a pleasure to be
of help.

Please let me know and I will try to send a message.

Bye,

Pierluigi Quagliotto

2014-08-31 13:02 GMT+02:00 Jaime Prilusky jaime.prilu...@weizmann.ac.il:

Bob,

Can you please provide a template letter?

Jaim

On Aug 31, 2014, at 1:45 PM, Robert Hanson hans...@stolaf.edu wrote:

Folks, I would appreciate some letter-writing support in relation to

http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0084.html
http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0377.html

I don't know if you can respond directly to that list or not. I think you
can. Please, if you do, be polite -- just share the importance of JSmol.
Ask them to remove the recommendation to browser developers to experiment
with breaking all our pages.

The executive summary is that if this recommendation is taken:

quote src=http://xhr.spec.whatwg.org/
Developers must not pass false for the async argument when the JavaScript
global environment
http://www.whatwg.org/specs/web-apps/current-work/multipage/infrastructure.html#javascript-global-environment
is a document environment
http://www.whatwg.org/specs/web-apps/current-work/multipage/webappapis.html#document-environment
as it has detrimental effects to the end user's experience. User agents are
strongly encouraged to warn about such usage in developer tools and may
experiment with throwing http://dom.spec.whatwg.org/#concept-throw an
InvalidAccessError http://dom.spec.whatwg.org/#invalidaccesserror
exception when it occurs so the feature can eventually be removed from the
platform.
/quote

All, and I mean ALL current JSmol implementations will stop working
instantly.

I'm not sure the writers of that understand the implications for science
and science education. Some word from others in prominent positions might
help.

I would prefer they not just hear from me. Don't over-do it, just help
them see what such experimentation would do to us.

That said, I am making good progress making FUTURE JSmol implementations
totally asynchronous. I'm actually very close. I have a test version that
loads everything asynchronously other than shapes, and it almost works.
(Famous last words!)

But current pages using Jmol.getPropertyAsArray() or Jmol.evaluateVar()
will absolutely be broken and will need some rewriting *even if I do get
a totally asynchronous version of JSmol running. *Because those are
inherently synchronous methods, and at least their first use requires an
asynchronous process.

I do have some ways around that. Basically you can effect (asynchronous)
module loading in Jmol (the to-be asynchronous part) by issuing calls to
Clazz._4Name(). For instance:

Clazz._4Name(JV.PropertyManager)

just after applet creation will load the code that will later be used
for Jmol.getPropertyAsArray() or Jmol.evaluateVar()

But obviously this will take updating of current web pages.

Bob

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Re: [Jmol-users] support needed -- XHR -- asynchronous vs synchronous

2014-08-31 Thread Pierluigi Quagliotto

Ok I will take into account of your suggestion.

The answer to the third question is nearly simple. Due to the little
experience in programming this would destroy the previous work and
probably, if the solution would not be easy to be applied, could also bring
the site to death.

Do you think that sending an URL from my site could help to explain how
simply JMol/JSMol can be used for teachng?

Since my University IT did not give me complete visibility outside the
university, I rented a server for a trial. Please see:
http://37.59.41.134/teaching-site and let me know... This is Joomla site
for which I asked you some info, a few months ago. Now I worked on the
basic development to ensure that JMol could be used properly. Luckily i
succeded to let it work in Joomla 2.5 (having Long Term Life support) and
the new Joomla 3.3.3 (having still Short Time support).

The English part is working, apart for a few things to be adressed. The
only menu item that need to be modified is  about configruatinal
steroisomers E / Z.

If you think and agree that can be of value to be used as an example, we
could stress that all this is nearly ready for a course to be started in
October and that this should be heavily revised in a too short time to
deliver an important tool for students... ..if by tomorrow the browsers
would reject the essential functonality of JMol...

If this can be used I will try to complete the English version in order to
be working, before sending the message.

Let me know and I will proceed to prepare a message that I will let you
have in order to check it before sending, since this matter is crtical.

Bye,

Pierluigi


2014-08-31 22:19 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 Sure. That's another great suggestion.  A third question is pertinent:

 As a scientist or educator, but not a programmer, how disruptive would it
 be for you if the next Firefox or Chrome or Safari or whatever browser
 follows through on the suggestion of this group to experiment with the
 proposed changes, thus shutting down all JSmol pages implemented to date?




 On Sun, Aug 31, 2014 at 8:30 PM, Pierluigi Quagliotto 
 pierluigi.quaglio...@unito.it wrote:

 Dear Bob,

 Would it be opportune and sufficient an intervention by someone like me,
 who have not so great programming skills? I could  stress the importance of
 JMol/JSMol even for simple projects devoted to education and knowledge
 spreading in the chemisty and biology fields, not much, probably... ...but
 if you think that the users can play a role, it would be a pleasure to be
 of help.

 Please let me know and I will try to send a message.

 Bye,

 Pierluigi Quagliotto


 2014-08-31 13:02 GMT+02:00 Jaime Prilusky jaime.prilu...@weizmann.ac.il
 :

  Bob,

  Can you please provide a template letter?

  Jaim

  On Aug 31, 2014, at 1:45 PM, Robert Hanson hans...@stolaf.edu wrote:

   Folks, I would appreciate some letter-writing support in relation to

 http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0084.html
 http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0377.html

  I don't know if you can respond directly to that list or not. I think
 you can. Please, if you do, be polite -- just share the importance of
 JSmol. Ask them to remove the recommendation to browser developers to
 experiment with breaking all our pages.

  The executive summary is that if this recommendation is taken:

 quote src=http://xhr.spec.whatwg.org/
 Developers must not pass false for the async argument when the JavaScript
 global environment
 http://www.whatwg.org/specs/web-apps/current-work/multipage/infrastructure.html#javascript-global-environment
 is a document environment
 http://www.whatwg.org/specs/web-apps/current-work/multipage/webappapis.html#document-environment
 as it has detrimental effects to the end user's experience. User agents are
 strongly encouraged to warn about such usage in developer tools and may
 experiment with throwing http://dom.spec.whatwg.org/#concept-throw an
 InvalidAccessError http://dom.spec.whatwg.org/#invalidaccesserror
 exception when it occurs so the feature can eventually be removed from the
 platform.
  /quote

  All, and I mean ALL current JSmol implementations will stop working
 instantly.

  I'm not sure the writers of that understand the implications for
 science and science education. Some word from others in prominent positions
 might help.

 I would prefer they not just hear from me. Don't over-do it, just help
 them see what such experimentation would do to us.

  That said, I am making good progress making FUTURE JSmol
 implementations totally asynchronous. I'm actually very close. I have a
 test version that loads everything asynchronously other than shapes, and it
 almost works. (Famous last words!)

 But current pages using Jmol.getPropertyAsArray() or Jmol.evaluateVar()
 will absolutely be broken and will need some rewriting *even if I do
 get a totally asynchronous version of JSmol running. *Because those

Re: [Jmol-users] Adding double bonds to Jmol's loading of PDB files and formatting said double bonds

2014-09-27 Thread Pierluigi Quagliotto

In effect, it would be interesting to set up JMol to use aromatic
character as a default when it has to work with organic structures.

When I use it in the classical way, receving the molecule from  JSME
through a call to an external server (NIH server), the 3D model shows
the double ond sof benzene as common double bonds. Is there  a way to
set up by which the aromatic rings can be displayed in a way that can
show immediately that the are aromatic (i.e. with an internal double
bond with respect to the ring)?

Just to see:
http://37.59.114.153/STdM/index.php/it/esercizi/disegnare-molecole-in-2d-e-3d

to draw some aromatic molecule and see how the 3D molecule is
displayed in JSMol.

If you have some further suggestion to improve how the molecule is
displayed, it would be nice for me to chenge my code to show to the
users better images.

Note that the site is still in final developing and the english part
should be totally revised ( it comes from automatic  translation  by
Google directly driven by Joomla) and some modification should be made
to introduce in the head the required javascript declarations, so the
english pages do not work properly at this moment.

Many thanks to all for you help and advices,

Bye,

Pierluigi

Il sabato 27 settembre 2014, Brenton Horne brentonho...@ymail.com ha
scritto:

 Hi Angel

 Thanks for the tip; but I have looked up the connect function in the
 user guide and I don't know how [atom-expression] and [bond-type] is
 meant to look like for my example. My current example is metamizole and
 I'd like a double bond to go between C17 and C18, any idea what code I'd
 have to use?

 Thanks for your time,
 Brenton

 On 27/09/2014 6:26 PM, Angel Herráez wrote:
  Hi Brenton
 
  1. If you edit manually the pdb file, you can add CONECT records for the
  double bonds. But it is better -and more flexible- to use Jmol scripts
 (which
  may be embedded in the pdb file or applied from within the page) with the
  connect command. This allows to set partial and aromatic bonds.
 
  2. Jmol has calculate aromatic and connect aromatic. You may or not
 like
  how they look, but it is the same idea as in your example.
  You could also draw a ring inside the atom ring (cycle) to depict
 aromaticity;
  that is not automatic, but a decoration you might build using the draw
  command.
 
 
 
 
 
 
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Re: [Jmol-users] Pure Fun Project

2015-01-09 Thread Pierluigi Quagliotto

Dear Othis,

I think that this could be more than a simple... just for fun!

Just to be clearer.. I am teaching Organic Chemistry and this could be
interesting to let student to build and optimize very simple molecules as
substituted benzenes, just to touch and learn the charge distribution
with MEP surfaces If it was possible to make very simple semi-empirical
calculations to let student to see and interact with the molecular
orbitals, this could be of great help for them and for the teacher also...

Wonderful job! Please let us know about novel improvements

Bye,

Pierluigi Quagliotto

2015-01-09 21:43 GMT+01:00 Otis Rothenberger osrot...@chemagic.com:

 There was no reason for this project other than pure fun, but the result
 might be of interest to some iPad users. The pure fun project related to
 this question: Would it be possible to write a mini virtual molecular model
 kit on an iPad, including server upload and site maintenance? It turns out
 it was easier than I thought:

 http://chemagic.com/molecules/

 Two apps to reference on this project:

 1) Textastic: A pure HTML/JS editor.
 2) HTML Egg Pro - A WYSIWYG editor - *sorta*!

 The latter is the strangest WYSIWYG editor I have ever seen. It has a
 fairly steep learning curve, but after a while you find yourself saying,
 Oh, now I get it. Basically, it's a pure touch/drag object editor with
 styles being calculated on the fly as you work. JS is put into the page in
 touch/drag object blocks. Both apps have FTP server upload.

 I'm not sure why I posed the question in the first place, but answering it
 was fun. I'm calling it VMK Mini, but I thought about calling it VMK
 Starbucks.

 Otis

 --
 Otis Rothenberger
 o...@chemagic.com


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Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

2016-03-24 Thread Pierluigi Quagliotto

Dear Bob,

many thanks!

I will update the JSMol version on my site and I will try to implement this
feature.

It should be amazing to have a naming feature that could give IUPAC names
to every (almost...) structure we can draw. I will imagine this is quite
difficult to implement.

However this naming feature based on NCI database is very interesting, at
least to give students and visitors of my site to have a chance to find a
coorect name. The other option to have a name is to draw a structure, and
naming it with the student ability and let the student to check it by using
OPSIN to get the structure. if the name is correct the structure will be
the same the student has drawn. A bit more complicated, but the students
could improve their ability in writing formulas correctly and naming them.

I will elt you know about the improving of my site.

Thanks again and bye!

Pierluigi

2016-03-23 19:42 GMT+01:00 Robert Hanson :

> Nothing stops you from adding that to your pages, Pierluigi! :)
>
> In answer to the question, the name/SMILES, SMILES/name and
> SMILES/structure conversion is going through the NCI CACTVS resolver, which
> is just a fantastic resource.
>
> structure/SMILES conversion is done within Jmol unless it is
>
>  print {*}.find("SMILES/NCI")
>  print {*}.find("SMILES/canonical")
>
> (these are just two ways of requesting the same thing)
>
>  in which case it goes through NCI
>
>
> Bob
>
> 
>
>
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Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

2016-03-23 Thread Pierluigi Quagliotto

Dear Bob and dear all,

is it possible to use the same feature in JSmol associating it to a
button?. It would be interesting to use it to help students during
nomenclature exercises.

Thanks!

Pierluigi


2016-03-22 19:04 GMT+01:00 Luciano Abriata :

> Robert, no, I didn't know. And it's amazing!
>
> Can you briefly and very plainly explain how the find() works? I mean,
> what's at the core of the formula-name-smile-etc conversions?
> Luciano
>
>
> --
> *De:* Robert Hanson 
> *Para:* "jmol-users@lists.sourceforge.net" <
> jmol-users@lists.sourceforge.net>
> *Enviado:* Martes, 22 de marzo, 2016 15:39:24
> *Asunto:* [Jmol-users] fun with Jmol -- .find("chemical",...)
>
> Did you know that this is now possible in Jmol:
>
> $ print "C1=CC=CC1=O".find("chemical","name")
> cyclopenta-2,4-dien-1-one
> $ print "succinic anhydride".find("chemical","SMILES")
> O=C1CCC(=O)O1
> $ print "maleic anhydride".find("chemical","SMILES")
> O=C1OC(=O)C=C1
> $ print "maleic anhydride".find("chemical","inchikey")
> FPYJFEHAWHCUMM-UHFFFAOYNA-N
> $ print "cholesterol".find("chemical","inchi")
>
> 1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
>
> 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] fun with Jmol -- xxxx.find("chemical",...)

2016-05-10 Thread Pierluigi Quagliotto

Dear All,

many thanks for your kind attention and all time you lost to give me some
info about the whole problem,

I had a look to the pages Otis and Bob linked, referring also to the new
topic "Let's Not Forget PubChem".

First of all, I was not fully aware of the integration of OPSIN into the
Resolver. The integration now is at the 1.2 version, while on the OPSIN
site it is claimed that OPSIN 2.1.0 was  released in March, 2016.

I tried the page Otis has just set-up and this is a very interesting way to
help student in determining the name by using both the Resolver and
PubChem. Unfortunately, by writing a few structures the Resolver or even
both the Resolver and PubChem failed to attribute a name. I have used also
structures from my DB and some of them could not be solved by both sites..


1) 7-ethyl-3,5-dimethyl-4-propyldodecane

2) 3-chloro-3-ethyl-4-methylpentanoic acid



Luckily, I tried directly on the OPSIN site and these structure were solved
and all representation were produced, starting from the name that I
indicated on my site as the solution.
I read on the Resolver site that OPSIN is the first trial to solve the
problem and after the Resolver works around the problem to solve it using
other ways. This should let the possibility that the structure that now
made the two sites to fail, should give good results, once the Resolver
will update to this version of OPSIN.

2016-05-09 20:48 GMT+02:00 Robert Hanson :

> I note that JSmol now includes a client-side InChI calculator. See
>
> http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm
>
> for more.
>
> Bob
>
> On Mon, May 9, 2016 at 12:51 PM, Otis Rothenberger 
> wrote:
>
>> One more JSME point on this subject. The JSME call backs that I mentioned
>> in this chain can handle the IUPAC dynamically as the structure is edited.
>> Again, here are all the new callbacks:
>>
>> BeforePaste, AfterPaste, AfterStructureModified, AtomHighlight,
>> BondHighlight, AtomClicked, BondClicked
>>
>> Any on these callbacks could be use to communicate with Resolver and
>> place the IUPAC  directly in JSME - i.e. the info holder bottom left. The
>> logical callbacks for IUPAC would be AfterStructureModified and/or
>> AfterPaste. Returned ResolverData after AJAX can be shown via:
>>
>> document.JME.showInfo(ResolverData)
>>
>> VERY IMPORTANT RESOLVER POINT IN ALL OF THIS:
>>
>> Resolver is not calculating these IUPAC’s. It is looking them up! This
>> goes back to the Herculean (to me) task of indexing all Volhardt compounds.
>> In Markus’ own words from his again viewable blog:
>>
>>
>> “We took great care during the implementation of the name index for this
>> web service, however, we are aware of that it is far from perfect and has
>> quite  few errors in it. Unfortunately, these errors are not easy to to
>> find if you have to deal with millions of names and their proper assignment
>> to the correct chemical structure. If you find any mistakes, please tell
>> us. Our plan is to improve the name index over the time but we are of
>> course happy about any contributions helpful for this process. Thanks!”
>>
>> And yes, he is talking about trivial AND IUPAC names above.
>>
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>>
>> On May 9, 2016, at 1:24 PM, Robert Hanson  wrote:
>>
>>
>>
>> On Mon, May 9, 2016 at 11:39 AM, Otis Rothenberger 
>> wrote:
>>
>>> Hi Pierluigi-
>>>
>>> For reasons that I do not fully understand, OPSIN returns InChI - not
>>> standard InChI. It does, however, return standard InChIKey! In general, I’d
>>> be very nervous about comparing InChI strings created by different
>>> resources.
>>>
>>>
>> NCI Resolver returns both.  You just have to ask for the right one.
>>
>> https://cactus.nci.nih.gov/chemical/structure/biphenol/stdinchi
>>
>> not
>>
>> https://cactus.nci.nih.gov/chemical/structure/biphenol/inchi
>>
>> I made that correction in Jmol some time back.
>>
>> Jmol has a broad range of comparison functions that do exactly what you
>> want to do. Take a look at the find() and compare() functions. Also note
>> the JSME needs to be carefully set up to deliver the right sort of SMILES.
>> See  jsmol/jsmetest.htm and jsmol/jsmetest2.htm in the distribution.
>>
>>
>>
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Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

2016-05-08 Thread Pierluigi Quagliotto

Dear Bob,

Last year I developed my teaching site:

http://www.iorgchem.unito.it

I am trying to see if it is possible to implement the use of JSME as the
2D editor, JSMol as the 3D viewer and OPSIN as the naming "resolver". Since
I am, however, a beginner as a programmer, I will have to test a lot the
code I will produce, in order to see if I can obtain something useful.
Since in my site the molecules used for quizzes are stored into a DB
(prepared with MolDB6), I could imagine at least two possibilities:

1) to prepare one page in which students can use my DB with already
available molecules for which the SMILES and Inchi  are already present
(calculated by MolDB6 when molecules are inserted into the DB). When
students submit a name for the molecule, OPSIN would calculate the Inchi
and by simple comparison with the given Inchi, it would be possible to know
if the answer is correct or not.

2) to prepare a page in which the user / student can draw its own molecule
and try to name it. In this case I would use directly JSmol to calculate
the Inchi. by comparison with the OPSIN derived Inchi, the user would
obtain the feedback about his answer.

My question is about the JSMol capabilities. I looked at your definition of
the function of JSMol to obtain the Inchi. I would be certain that JSMol
can convert a SMILES into Inchi, without using the NCI resolver. Am I
right about this feature or the resort to NCI resolver is needed? This is a
fantastic resource, but only molecules inside to its DB can be found and
named. My goal would be to give everyone the possibility to find a name for
a molecule, within the capabilities of OPSIN. It would be also interesting,
if this idea could be implemented, to include OPSIN into the programs of
the JSMol release, obviously if the JSMol and OPSIN  licenses can agree
each other.

This should be a definite way to give JSmol all the power for organic
chemistry teaching.

Sorry for my long message, I am quite "verbose"

Many thanks for your attention and your huge effort to develop a wonderful
piece of software!

Pierluigi

2016-03-24 14:48 GMT+01:00 Robert Hanson <hans...@stolaf.edu>:

> Great, yes.
>
> I use this feature in class a lot when  I am teaching organic chemistry.
>
> On Thu, Mar 24, 2016 at 4:05 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear Bob,
>>
>> many thanks!
>>
>> I will update the JSMol version on my site and I will try to implement
>> this feature.
>>
>> It should be amazing to have a naming feature that could give IUPAC names
>> to every (almost...) structure we can draw. I will imagine this is quite
>> difficult to implement.
>>
>> However this naming feature based on NCI database is very interesting, at
>> least to give students and visitors of my site to have a chance to find a
>> coorect name. The other option to have a name is to draw a structure, and
>> naming it with the student ability and let the student to check it by using
>> OPSIN to get the structure. if the name is correct the structure will be
>> the same the student has drawn. A bit more complicated, but the students
>> could improve their ability in writing formulas correctly and naming them.
>>
>> I will elt you know about the improving of my site.
>>
>> Thanks again and bye!
>>
>> Pierluigi
>>
>> 2016-03-23 19:42 GMT+01:00 Robert Hanson <hans...@stolaf.edu>:
>>
>>> Nothing stops you from adding that to your pages, Pierluigi! :)
>>>
>>> In answer to the question, the name/SMILES, SMILES/name and
>>> SMILES/structure conversion is going through the NCI CACTVS resolver, which
>>> is just a fantastic resource.
>>>
>>> structure/SMILES conversion is done within Jmol unless it is
>>>
>>>  print {*}.find("SMILES/NCI")
>>>  print {*}.find("SMILES/canonical")
>>>
>>> (these are just two ways of requesting the same thing)
>>>
>>>  in which case it goes through NCI
>>>
>>>
>>> Bob
>>>
>>> 
>>>
>>>
>>> --
>>> Transform Data into Opportunity.
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>>>
>>>
>>
>>
>> ---

Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

2017-04-09 Thread Pierluigi Quagliotto


Many thanks, Bob!

Bye!

Pierluigi


Il 08/04/2017 03:54, Robert Hanson ha scritto:

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/


Jmol.___JmolVersion="14.12.1"

bug fix: NBO update
bug fix: JavaScript bug - missing  Math.signum(f) - causes 
{atom}.chirality to not work in JSmol


JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- also SELECT chirality = 'R'# or SELECT chirality != ""
  -- uses Cahn-Ingold-Prelog rules to assign R or S to a carbon center
  -- ignores sulfur chirality
  -- may not fully implement high symmetry cases
  -- not fully tested



--
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] R: Re: Jmol 14.12.1 released -- R/S chirality


Il 09/04/2017 21:16, pinostricc...@alice.it ha scritto:
Great job, Bob. Really. I will implement it on my website for my 
students to use.

Sometime imagining molecules in 3D is not that easy :)
@Pierluigi. I was referring to your pages too with my compliment
Pino

Messaggio originale
Da: hans...@stolaf.edu
Data: 9-apr-2017 14.55
A:
"jmol-users@lists.sourceforge.net"<jmol-users@lists.sourceforge.net>
Ogg: Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

I will release another version of Jmol later today that has been
pretty heavily validated using some excellent  extreme examples
provided by Mikko Vainio that caught a couple of bugs.

On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto
<pierluigi.quaglio...@unito.it
<mailto:pierluigi.quaglio...@unito.it>> wrote:

Many thanks, Bob!

Bye!

Pierluigi



Il 08/04/2017 03:54, Robert Hanson ha scritto:


https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/

<https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/>


Jmol.___JmolVersion="14.12.1"

bug fix: NBO update
bug fix: JavaScript bug - missing Math.signum(f) - causes
{atom}.chirality to not work in JSmol

JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- also SELECT chirality = 'R'# or SELECT chirality != ""
  -- uses Cahn-Ingold-Prelog rules to assign R or S to a
carbon center
  -- ignores sulfur chirality
  -- may not fully implement high symmetry cases
  -- not fully tested



-- 
Robert M. Hanson

Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
<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
<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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Dear all,

the page I was started to draw about chirality and that inspired Bob to 
develop the chirality recognition functions in JMol is now ready on my 
site at the address:


http://www.iorgchem.unito.it/index.php/en/exercises/practice-on-chirality

Every suggestion / criticism is welcome.

Please note that student should learn the procedure by simply following 
the instructions reported just above the JSME /JSMol panel.


The button Reset was inserted to reset the status of the label 
background after the first check of the answer, since a yellow 
background would be still present when a new trial is done. The student 
that made a mistake can start again without showing a yellow background 
for the label he is introducing on the chiral carbon. The  yellow 
background is intended  for the final "correct" answer only.


Bye,

Pierluigi

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Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

2017-04-06 Thread Pierluigi Quagliotto


Dear Bob,

many thanks for your answer.
I had a look to the paper, but it is very concise, so I would be in 
doubt about how to proceed. If we (I and a young fellowship who should 
help me for the site in next months) can envisage what (and how to do) 
we will let you know some more. Obviously, if this feature will become 
available in JMol/JSMol, this should be nice and also a great 
improvement for teaching!


I will start to introduce the page I prepared in the production site, 
just to let student to familiarize with the common procedure used to 
approach to chirality determination. If some improvement about chirality 
determination will be available in JMol/JSMol in the future, I will use 
it enthusiastically. In the last two-three years, as long as my site 
teaching site was produced and developed, I observed great improvement 
in the student's ability to comprehend concepts and use them in solving 
problems, so I will try to do all my best to make continuous site 
improvements, as far as I am able to deal with programming.


Many thanks again for the time you dedicate to me,

Bye!

Pierluigi





Il 06/04/2017 14:29, Robert Hanson ha scritto:



On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto 
<pierluigi.quaglio...@unito.it <mailto:pierluigi.quaglio...@unito.it>> 
wrote:


Dear All,

I prepared a page for students (on my developing server:
http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-sulla-chiralita

<http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-sulla-chiralita>),
in which they can:

1) write down an organic molecule in  JSME

2) submit it to JSmol

3) attribute the Cahn-Ingold-Prelog priority to each group by
selecting
the first atom of each group which is attached to the Chiral
Carbon and
clicking on a button that create a label for that atom.

4) reorientate properly the molecule, in order to be able to
assign the
R / S configuration for chirality.

This is enough for me to use in classroom just to show how one should
proceed to work on exercises.


My question is: Is there a way to obtain priority (by CIP rules) for
each group attached to a Chiral Carbon? Is it possible to use some
JSmol
function(s) to obtain this information?


ho, ho! No, sorry. Can't do that. But I love the idea. In principal 
the algorithm is not all that difficult.

https://www.chemcomp.com/journal/chiral.htm Maybe it's time to add that...



If the answer is yes, this could help me to modify the page to
give the
student the chance to explore the correct result by viewing a
model with
correct priority labelling and also by clicking on a button which
activate a function that perform the check.


Sorry to bothering you...


Bye!


Pierluigi Quagliotto




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--
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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] check R/S chirality with Jmol


Dear Bob,

there is something working wrong with JSMol 14.12.0 working on my 
developing site...


I obtain an error in the console when trying to execute some commands.

here below the message is always the same and appears when the first 
call to the novel function is tried.


*

*

*Jmol now allows checking of R/S chirality. For example:

*
load $(R)-glycidol
print {C1}.chirality
script ERROR: TypeError: The object does not support the property or the 
method 'printStackTrace'




/R/

load $cholesterol
select on chirality != ""
script ERROR: TypeError: The object does not support the property or the 
method 'printStackTrace'



label %[chirality]

/8 atoms selected/




I simply transferred the jsmol dir on the server, as usual and gave 
proper 755 permission and apache.apache ownership. JSMol seems to work 
fine but ht euse of the new function gave this error.


Bye,

Pierluigi Quagliotto


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Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality


Many thanks, Pino!

If you like it, my page is now online on the production site at: 
http://www.iorgchem.unito.it. The page is in the menu Esercizi ---> 
Esercitarsi sulla Chiralità.


The page was now updated and the scope is to make students to follow the 
full path:


1) assign the labels to the chiral carbon, and to the 4 substituents.

2) orientate the molecule in the proper way

3) assign the chirality by selecting the chiral carbon and substituting 
the label C with R o S by clicking on the R or S button


4) check the chirality with the button "Controlla Chiralità"

At the present moment the page is intended to work for molecules having 
only one chiral carbon. I should write some function to manage more 
carbons (i.e the typical example of the cholesterol, should be a nice 
test!) by taking action on each as a separate case. If I will have some 
problem in managing this situation (it is not clear to me yet how to 
do...) I will ask you!


for all who are interested into it, the English version will be ready in 
a matter of minutes since I will present it to my student in less than 2 
hours!


 if someone has suggestions or find some bug, please let me know.


Bye! And happy JMol-iing with this novel feature!

Pierluigi

Il 09/04/2017 21:16, pinostricc...@alice.it ha scritto:
Great job, Bob. Really. I will implement it on my website for my 
students to use.

Sometime imagining molecules in 3D is not that easy :)
@Pierluigi. I was referring to your pages too with my compliment
Pino

Messaggio originale
Da: hans...@stolaf.edu
Data: 9-apr-2017 14.55
A:
"jmol-users@lists.sourceforge.net"<jmol-users@lists.sourceforge.net>
Ogg: Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

I will release another version of Jmol later today that has been
pretty heavily validated using some excellent  extreme examples
provided by Mikko Vainio that caught a couple of bugs.

On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto
<pierluigi.quaglio...@unito.it
<mailto:pierluigi.quaglio...@unito.it>> wrote:

Many thanks, Bob!

Bye!

Pierluigi



Il 08/04/2017 03:54, Robert Hanson ha scritto:


https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/

<https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/>


Jmol.___JmolVersion="14.12.1"

bug fix: NBO update
bug fix: JavaScript bug - missing Math.signum(f) - causes
{atom}.chirality to not work in JSmol

JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- also SELECT chirality = 'R'# or SELECT chirality != ""
  -- uses Cahn-Ingold-Prelog rules to assign R or S to a
carbon center
  -- ignores sulfur chirality
  -- may not fully implement high symmetry cases
  -- not fully tested



-- 
Robert M. Hanson

Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
<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
<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

Re: [Jmol-users] Jmol 14.13.1


Dear Bob,

many thanks for the crucial update!

Yesterday I have published on the site the page for the step-by-step 
chirality assignment procedure.


It should be intended for compound having only one chiral carbon since I 
did not implemented yet any function to take into account the presence 
of more chiral carbons.


the page which is present on the development site (only in italian) is 
working correctly with the "unofficial" jsmol.zip you prepared and gave 
us before making the finale 14.12.1 release.


http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-sulla-chiralita

while the page on the production site, running the 14.13.1 version, is 
showing an error for a call to a function:


[Javascript] The required class file

/jsmol/j2s/JU/BNode.js
could not be loaded. Script error. Syntax Error. and other things are 
following.


Did I write something in the scripts that now should be treated and 
written in another way? Or this is a bug?




Many tahnks ina dvance for your help!

Bye!

Pierluigi




Il 10/04/2017 04:44, Robert Hanson ha scritto:

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.13/Jmol%2014.13.1/

Jmol.___JmolVersion="14.13.1" // 2017.04.09

new feature: set labelfor {atomset} "value"
 -- allows setting of label without changing current selection
 -- uses same syntax as LABEL command after {atomset}
 -- for example:

   set labelfor @atoms @myLabel
   set labelfor {atomno <= 3} @{["a","b","c"]}
   set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"

new feature: MOL V2000 reader loads >  blocks into _M.molData

bug fix: {*}.chirality with triple bonds fails
bug fix: {*}.chirality fix for duplicated atoms check

bug fix: dotted line has annoying extra dot: measure ID m @1 @4 radius 0.1

bug fix: NBO H-BOND and MODEL focus issues



--
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] Jmol 14.13.1


Dear Bob,

Sorry... I forgot to add  the address of the production site:

http://www.iorgchem.unito.it/index.php/en/exercises/practice-on-chirality

bye!

Pierluigi

il 10/04/2017 04:44, Robert Hanson ha scritto:

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.13/Jmol%2014.13.1/

Jmol.___JmolVersion="14.13.1" // 2017.04.09

new feature: set labelfor {atomset} "value"
 -- allows setting of label without changing current selection
 -- uses same syntax as LABEL command after {atomset}
 -- for example:

   set labelfor @atoms @myLabel
   set labelfor {atomno <= 3} @{["a","b","c"]}
   set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"

new feature: MOL V2000 reader loads >  blocks into _M.molData

bug fix: {*}.chirality with triple bonds fails
bug fix: {*}.chirality fix for duplicated atoms check

bug fix: dotted line has annoying extra dot: measure ID m @1 @4 radius 0.1

bug fix: NBO H-BOND and MODEL focus issues



--
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] Jmol 14.14.1

2017-04-20 Thread Pierluigi Quagliotto


Many thanks, Bob!

Wonderful news! I am waiting for the availability of the release to 
imrpove my page on chirality and to prepare also a page to introduce all 
the steps needed to assign E/Z configurations.


Bye!

Pierluigi

Il 20/04/2017 06:28, Robert Hanson ha scritto:

Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently 
selected atoms by default)


new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when JSpecView 
is opened in Jmol

  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific 
file format)

  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol because some 
platforms cannot read them locally

  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC 
Rules 1, 2, and 3 (though still some questions about Rule 3)

bug fix: print getProperty("cifinfo") without file name fails




--
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] R: check R/S chirality with Jmol


Il 07/04/2017 19:38, Robert Hanson ha scritto:
I've added a "show R/S" button at 
https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm


It just runs

label %[chirality]
background labels yellow



On Fri, Apr 7, 2017 at 12:24 PM, Robert Hanson <hans...@stolaf.edu 
<mailto:hans...@stolaf.edu>> wrote:


I have that fixed in JavaScript but want to add a couple more
unrelated items before I release this the normal way. But you  can
also get jsmol.zip here:
https://sourceforge.net/p/jsmol/code/HEAD/tree/trunk/dist/
<https://sourceforge.net/p/jsmol/code/HEAD/tree/trunk/dist/> and
it should be  working at the St. Olaf site. For example:

<https://chemapps.stolaf.edu/jmol/jsmol/simple2.htm?load%20$(R)-2-butanol;label%20%[chirality];background%20labels%20yellow;set%20antialiasdisplay

<https://chemapps.stolaf.edu/jmol/jsmol/simple2.htm?load%20$%28R%29-2-butanol;label%20%[chirality];background%20labels%20yellow;set%20antialiasdisplay>>


On Fri, Apr 7, 2017 at 11:57 AM, pinostricc...@alice.it
<mailto:pinostricc...@alice.it> <pinostricc...@alice.it
<mailto:pinostricc...@alice.it>> wrote:

Wonderful implementation Bob and Pierluigi. Veru useful in
Organich Chemistry
Pino

Messaggio originale
Da: hans...@stolaf.edu <mailto:hans...@stolaf.edu>
Data: 7-apr-2017 4.25
A: "jmol-users@lists.sourceforge.net

<mailto:jmol-users@lists.sourceforge.net>"<jmol-users@lists.sourceforge.net
<mailto:jmol-users@lists.sourceforge.net>>
Ogg: [Jmol-users] check R/S chirality with Jmol

*Download Jmol-14.12.0-binary.zip (69.3 MB)

<https://sourceforge.net/projects/jmol/files/latest/download?source=files>


*
*Jmol now allows checking of R/S chirality. For example:

*
load $(R)-glycidol
print {C1}.chirality

/R/

load $cholesterol
select on chirality != ""
label %[chirality]

/8 atoms selected/


Thanks to Pierluigi Quagliotto for the suggestion to
tackle this. It was a good challenge getting it right.

Please test!

Bob

-- 
Robert M. Hanson

Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
<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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St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
<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




--
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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Dear Bob,


the jsmol.zip file you described in the last message, while not released 
is working like a charm, on my developing site! I will try to produce 
some buttons to extend the scope of the page and after a few test I will 
put on the production site for extended testing.



Many thank for all!


Bye!


Pierluigi

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Re: [Jmol-users] Cahn-Ingold-Prelog priority rules


Dear Bob,

many thanks for it!

In this weekend I will try  to update my page and make proper test. Once 
I will be able to put the page on the production site I will put my 
student to make extensive tests, with both simple and complex molecules, 
to help you to validate the novel function. I'll let you know when the 
page will be ready, just to see it "at work".


Bye!

Pierluigi Quagliotto

Il 07/04/2017 01:21, Robert Hanson ha scritto:

This is done.


Jmol.___JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
  -- ignores sulfur chirality
  -- may not fully implement high symmetry cases
  -- not fully tested
  -- Checked using:

function checkchiral(m) {
  if (m)  load @m
  background label yellow
  color labels black
  select _C
  label %[atomname]
  refresh
  var b = {_C}
  for (var a in b) {
var c = a.chirality;
print _smilesString + " " + a + c
if (c) {
   select a
   c = a.atomname + " " + c
   label @c
}
  }
  select *
}

checkchiral("$(R)-glycidol")
delay 1
checkchiral("$glucose")
delay 1
checkchiral("$(2S,3R)-2,3-oxiranediol")
delay 1
checkchiral("$(S)-2-butanol")
delay 1
checkchiral("$(R)-2-butanol")
delay 1
checkchiral("$(2S,3R)-2,3-butanediol")
delay 1
checkchiral("$(2S,3S)-2,3-butanediol")
delay 1
checkchiral("$(2R,3R)-2,3-butanediol")
delay 1
checkchiral("$(2R,3S)-2,3-butanediol")
delay 1
checkchiral("$1,4-dimethylcyclohexane")
delay 1
checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R




On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto 
<pierluigi.quaglio...@unito.it <mailto:pierluigi.quaglio...@unito.it>> 
wrote:


Dear Bob,

many thanks for your answer.
I had a look to the paper, but it is very concise, so I would be
in doubt about how to proceed. If we (I and a young fellowship who
should help me for the site in next months) can envisage what (and
how to do) we will let you know some more. Obviously, if this
feature will become available in JMol/JSMol, this should be nice
and also a great improvement for teaching!

I will start to introduce the page I prepared in the production
site, just to let student to familiarize with the common procedure
used to approach to chirality determination. If some improvement
about chirality determination will be available in JMol/JSMol in
the future, I will use it enthusiastically. In the last two-three
years, as long as my site teaching site was produced and
developed, I observed great improvement in the student's ability
to comprehend concepts and use them in solving problems, so I will
try to do all my best to make continuous site improvements, as far
as I am able to deal with programming.

Many thanks again for the time you dedicate to me,

Bye!

Pierluigi






Il 06/04/2017 14:29, Robert Hanson ha scritto:



On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto
<pierluigi.quaglio...@unito.it
<mailto:pierluigi.quaglio...@unito.it>> wrote:

Dear All,

I prepared a page for students (on my developing server:

http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-sulla-chiralita

<http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-sulla-chiralita>),
in which they can:

1) write down an organic molecule in  JSME

2) submit it to JSmol

3) attribute the Cahn-Ingold-Prelog priority to each group by
selecting
the first atom of each group which is attached to the Chiral
Carbon and
clicking on a button that create a label for that atom.

4) reorientate properly the molecule, in order to be able to
assign the
R / S configuration for chirality.

This is enough for me to use in classroom just to show how
one should
proceed to work on exercises.


My question is: Is there a way to obtain priority (by CIP
rules) for
each group attached to a Chiral Carbon? Is it possible to use
some JSmol
function(s) to obtain this information?


ho, ho! No, sorry. Can't do that. But I love the idea. In
principal the algorithm is not all that difficult.
https://www.chemcomp.com/journal/chiral.htm
<https://www.chemcomp.com/journal/chiral.htm> Maybe it's time to
add that...



If the answer is yes, this could help me to modify the page
to give the
student the chance to explore the correct result by viewing a
model with
    correct priority labelling and also by clicking on a button which
activate a function that perform the check.


Sorry to bothering you...


Bye!

Re: [Jmol-users] R: check R/S chirality with Jmol