from:"Jennifer L. Muzyka"

Bob,
I realize that Jmol uses Ajax.  So I’ve been using Ajax all along.  This was my 
first time I wrote the Ajax HTML and JavaScript myself to communicate with 
server-side PHP code I also wrote myself.  So it felt different to me.
Jennifer







Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jul 22, 2016, at 10:10 AM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:



On Fri, Jul 22, 2016 at 8:42 AM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
InChI is very messy because there’s more than one version of the program that 
generates it.  So depending on what version you use, you get a different InChI. 
 That information about which version of the InChI rules you are using is an 
early part of the string.  The other problem with InChI is that the strings can 
be REALLY LONG, as in so long that it’s not possible to use them when you 
search Google.  That was another take-away from the course.

You do have to define the rules so that you get the sections right. Beyond 
that, I suppose it may be true, but not for simple molecules. Any changes by 
version would be for esoteric species (I am guessing.) What you are saying 
violates the whole premise of InChI. Do you have examples, Jennifer?

2. Quick Facts
2.1. What is an InChI?

InChI is an acronym for IUPAC International Chemical Identifier. It is a string 
of characters capable of uniquely representing a chemical substance and serving 
as its unique digital ‘signature’. It is derived solely from a structural 
representation of that substance in a way designed to be independent of the way 
that the structure was drawn. A single compound will always produce the same 
identifier.

[http://www.inchi-trust.org/technical-faq/]


You are using AJAX every time you use JSmol. All files are transmitted using 
AJAX, and within JSmol you can do AJAX as simply as


x = load("http://..;)


I don't see why you would need any server-side piece these days. It is 
certainly not "elegant" in my opinion. Elegant is

if ("my SMILES string".find("your SMILES string", "SMILES")) prompt "You're 
good to go!"


without any concern for where the strings come from. That's what JSmol does. No 
server required. Just make sure you are using  the right  options in JSME. See 
http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm


}

var JMEInfo = {
use: "HTML5"
  ,visible: true
  ,divId: "jmediv"
  ,options : "autoez;nocanonize"


}


Here's a note I have on that from an earlier jmol-users post:

JSME and 2D/3D -  It turns out that JSME has two modes of delivery of SMILES -- 
"canonize" and "nocanonize"...The problem is that "canonize" delivers aromatic 
symbols for rings that  are not huekel-aromatic -- all six carbons, for 
example, in benzoquinone. Jmol does this, too, but Jmol adds double bond 
indications as well, so ...c=cc=c The difference is significant -- Jmol's 
SMILES representations are interpretable by the NCI Resolver; JSME's "canonize" 
versions are not. So I  have to have JSME in nocanonize mode in order to 
convert 2D to 3D using the NCI Resolver.

Bob





--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JSME and SMILES

Here’s the documentation that served as the reading for the fall 2015 OLCC
course on cheminformatics, from
http://olcc.ccce.divched.org/2015OLCCModule5P1#3.2
Because the layered structure of InChI allows one to represent a chemical
structure with a desired level of details, InChI software may generate
different InChI strings for the same molecule. This flexibility may be
regarded as an obstacle to standardization and interoperability. In response
to this concern, the standard InChI was introduced which contains the same
level of structural details and the same conventions for drawing perception, by
using standard option settings in InChI software. The standard InChI
representations begin with “InChI=1S/”, while the non-standard InChI begins
with “InChI=1/”. The digit “1” following “InChI=” is the current InChI version
number.

InChIKey

The length of an InChI string increases with the size of the corresponding
chemical structure, and it is very common that molecules with more than 100
atoms result in very long InChI strings, which are not appropriate to use in
internet search engines (such as Google, Yahoo, Bing, and so on). In addition,
these search engines do not care about case sensitivity nor special characters
used in InChI. To address this issue, the InChIKey was introduced for Internet
and database searching/indexing. It is a 27-character string derived from
InChI, using a hashing algorithm. Hashing is a one-way mathematical
transformation typically used to calculate a compact fixed length digital
representation of a much longer string of arbitrary length.

I guess I paid more attention to the phrase about “obstacle to standardization
and interoperability” than I did to the part about it being “molecules with
more than 100 atoms” having long InChI strings.
Jennifer

Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY 40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925

On Jul 22, 2016, at 10:10 AM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:

On Fri, Jul 22, 2016 at 8:42 AM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
InChI is very messy because there’s more than one version of the program that
generates it. So depending on what version you use, you get a different InChI.
That information about which version of the InChI rules you are using is an
early part of the string. The other problem with InChI is that the strings can
be REALLY LONG, as in so long that it’s not possible to use them when you
search Google. That was another take-away from the course.

You do have to define the rules so that you get the sections right. Beyond
that, I suppose it may be true, but not for simple molecules. Any changes by
version would be for esoteric species (I am guessing.) What you are saying
violates the whole premise of InChI. Do you have examples, Jennifer?

2. Quick Facts
2.1. What is an InChI?

InChI is an acronym for IUPAC International Chemical Identifier. It is a string
of characters capable of uniquely representing a chemical substance and serving
as its unique digital ‘signature’. It is derived solely from a structural
representation of that substance in a way designed to be independent of the way
that the structure was drawn. A single compound will always produce the same
identifier.

[http://www.inchi-trust.org/technical-faq/]

You are using AJAX every time you use JSmol. All files are transmitted using
AJAX, and within JSmol you can do AJAX as simply as

x = load("http://..;)

I don't see why you would need any server-side piece these days. It is
certainly not "elegant" in my opinion. Elegant is

if ("my SMILES string".find("your SMILES string", "SMILES")) prompt "You're
good to go!"

without any concern for where the strings come from. That's what JSmol does. No
server required. Just make sure you are using the right options in JSME. See
http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm

}

var JMEInfo = {
use: "HTML5"
,visible: true
,divId: "jmediv"
,options : "autoez;nocanonize"

}

Here's a note I have on that from an earlier jmol-users post:

JSME and 2D/3D - It turns out that JSME has two modes of delivery of SMILES --
"canonize" and "nocanonize"...The problem is that "canonize" delivers aromatic
symbols for rings that are not huekel-aromatic -- all six carbons, for
example, in benzoquinone. Jmol does this, too, but Jmol adds double bond
indications as well, so ...c=cc=c The difference is significant -- Jmol's
SMILES representations are interpretable by the NCI Res

Re: [Jmol-users] JSME and SMILES

InChI is very messy because there’s more than one version of the program that 
generates it.  So depending on what version you use, you get a different InChI. 
 That information about which version of the InChI rules you are using is an 
early part of the string.  The other problem with InChI is that the strings can 
be REALLY LONG, as in so long that it’s not possible to use them when you 
search Google.  That was another take-away from the course.

The reason I have been using server side lookup for the current page I’m 
developing is that I’m having students draw the starting material for a given 
reagent/product combination.  There are often numerous starting materials that 
are possible.  Going back to the server seemed much more elegant than trying to 
manage regular expressions on the variety of different SMILES or adding a 
second query to generate a complete list of other possible starting materials 
that would also work.  And it was cool to me because it forced me to finally 
learn how to do Ajax.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jul 22, 2016, at 9:28 AM, Robert Hanson 
> wrote:

It's a very odd use of the word "canonical." I'm surprised you came away with 
that understanding, because the fact that it is the way I describe is well 
documented and very important.

InChI is truly canonical, mostly because there is exactly one program/algorithm 
in the world that can create it. Now that that is available in JavaScript (and 
is in the JSmol distribution -- see 
http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm or in your jsmol folder of the 
distribution) there is no need for any server-side business for many 
applications.

InChI keys are just hashes of InChIs. I guess there is some possibility that 
they are not unique (two molecules can have the same hash code, just as any two 
ASCII strings can). For your purposes those would work as well.

I have not experimented with making hashes from inchi.js, but I am sure it is 
possible. It's a very simple process once you have the InChI key.

Bob


--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JSME and SMILES

Bob,
I was under the impression that canonical SMILES would be the same from one 
program to another, not just from the same program.  I participated in the Fall 
2015 OLCC on cheminformatics, and that’s what I remember us teaching the 
students.  So the distinction you are making is reasonable to me but a new idea.

It’s wonderful to hear that Jmol could convert the SMILES to InChI with such an 
easy process.  Can it also do InChIKey?  The cheminformatics guys made a big 
deal over that being better than InChI in the OLCC course.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jul 22, 2016, at 9:01 AM, Robert Hanson 
> wrote:

Hi, Jennifer.

"Canonical" SMILES just means that a given version of a given program will 
always report out the same string for a compound. Key words there are "same 
program" and "same version". So if you used an earlier version of a program to 
create a database of strings to compare, then you probably need to run through 
that set with any newer version of JSME and require users use that version.

In developing the SMILES capabilities of Jmol I decided not to even attempt 
canonicalization. It has not been important for any application I have seen, 
short of what you are doing -- database lookup. But for that you can use InChI 
keys. Jmol can deliver those either from the browser using inchi.js or by 
remote calls to the NCI Resolver.

If you have only 3000 compounds, you could set up a little 5-line script that 
will run in Jmol.jar that will probably take 10 minutes to convert all SMILES 
to InChI.

Bob

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Quiz Answers: Shhh, tell no one

2016-07-20 Thread Jennifer L. Muzyka

Thanks for this encryption code, Otis!

All along I've been skeptical about issues comparing strings, especially since 
I would get them from JSME. Now I figured out how to get JSME to spit out 
SMILES with slashes for E/Z stereochem. And I see that comparing those strings 
is a big problem.  Even JavaScript hiccups on the backslashes. 

Mike, if you're willing to share hidden div Jmol SMILES comparison code with 
me, I'd appreciate it. And I'm psyched to see the cool stuff you're doing with 
ChemDoodle and curly mechanism arrows on your site. 
Jennifer

Sent from my iPhone

> On Jul 20, 2016, at 5:12 PM, Otis Rothenberger  wrote:
> 
> Mike and Jennifer,
> 
> Previous chain getting too long (bounce long!), and none of us truncated - 
> sorry!
> 
> Re Quiz Answers, S, tell no one...
> 
> This is a classic encryption technique that’s weak and easy for 
> cryptographers to break. Your students will never figure it out! It makes use 
> of the obscure (and obtuse) XOR logic operator (^). Basically, it diddles 
> ascii character binary bits in such a way that the encryption and decryption 
> functions are one and the same. The encrypted data (see code below) is stored 
> in globalAnswerHolder. While this is a string, don’t try to view it. It can 
> contain many non-printable characters. The intKey argument is simply an 
> integer encryption key - e.g. 100. Actually, it’s the integer’s binary 
> equivalent that is the key.
> 
> var globalAnswerHolder;
> function encryptAndDecrypt(strDataToProcess, intKey) {
>var strBuilder = "";
>for(i=0;i < strDataToProcess.length;i++) {
>strBuilder += String.fromCharCode(intKey ^ 
> strDataToProcess.charCodeAt(i));
>}
>globalAnswerHolder = strBuilder;
> }
> 
> Just pass globalAnswerHolder through the function again to decrypt.
> 
> Of course your students could do this also, so obscure the function:
> 
> var theBoyCouldPlay;
> function Ish(Mark, Knopfler) {
>var Kabbible = "";
>for(i=0;i < Mark.length;i++) {
>Kabbible += String.fromCharCode(Knopfler ^ Mark.charCodeAt(i));
>}
>theBoyCouldPlay = Kabbible;
> }
> 
> Your students will be in Comedic Dire Straits (ouch)!
> 
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
> 
> 
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are 
> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
> reports.http://sdm.link/zohodev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] JSME and SMILES

2016-07-20 Thread Jennifer L. Muzyka

Thanks, Mike.  Your explanation finally helps me understand why Otis is so 
focused on having Jmol do the comparisons rather than going back to the 
database.  I didn’t get that until now.  The potential complication for me is 
that I’m hoping to eventually implement these questions in a graded homework 
system.  I realize that students are resourceful and having the SMILES in the 
page’s JavaScript would make it possible (not actually easy) for students to 
cheat.  So I’m reluctant to have the SMILES in the page.  Is there a way to do 
the Jmol SMILES comparison on the server side?
Jennifer








On Jul 20, 2016, at 7:09 AM, Mike Casey 
<mike.ca...@ucd.ie<mailto:mike.ca...@ucd.ie>> wrote:

Hi Jennifer & Otis,

I'm a relatively inexperienced programmer so please treat the following with 
caution.  However, FWIW, I use the approach that Otis is recommending (if I 
understand him correctly).  Users make selections, ajax is used once to 
retrieve all the data relevant to a problem of the appropriate type from a 
database (as a JSON object that is easy to work with in Javascript).  The 
structures drawn by the user in JSME are then checked by comparison of the user 
SMILES from JSME against the correct SMILES, retrieved from the database with 
the other problem data, using Jmol (which is in a hidden div on the page.  As 
Otis says, Jmol matches different SMILES strings from different sources as long 
as the structures are the same.  My site is not in the wild yet (it is a major 
upgrade of http://www.ucd.ie/chem/chemint/), but I would be happy to send the 
code to you if that would be helpful.

Mike


Dr Mike Casey
School of Chemistry
UCD
Dublin
01 716 2420

On 20 July 2016 at 01:58, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:
Jennifer,

The student SMILES and the answer SMILES need to be compared on the client 
(browser) side via JavaScript. The student answer SMILES is already on the 
client side. All we would need is the answer SMILES there also.

Having said this, I know that Bob H once mentioned running the Java app on the 
server to do server side tasks, but running the Java app on the server is way 
beyond my programming skills.

With the power of modern JavaScript and HTML5, I’m not sure I see why the 
computer jocks are more comfortable with a second hit on the server. The fact 
is that the server cannot do the SMILES comparison as elegantly as Bob’s JSmol 
SMILES comparison, that is unless the Jmol Java App is run on the server. With 
the client side JavaScript/HTML5 power, it seems to me going back to the server 
is just going back to the server in order to go back to the server!

All of this, of course, is dependent on getting the answer SMILES into the 
working webpage.

Whichever route you go, that still leaves you with a database with some SMILES 
issues. Here’s a suggestion: How soon is Bob B’s cheminformatics course going 
into action again? Reconstructing your database entirely from Resolver (maybe 
PubChem) by an automated process would be a great real world project for one of 
the student teams. ( cc to Bob B)

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 8:22 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
What you are describing is essentially how I handle the code for the page where 
students draw the product structure.  It's certainly doable for the starting 
material structure as well.  I would just need to work out the different query 
and JavaScript.  My computer science colleagues would probably consider that 
the brute force method, unlike the more elegant Ajax method that goes back and 
queries the database a second time.  Is there some advantage to keeping all of 
the code within the page rather than going back to the database?  Those use PHP 
and MySQL.
Jennifer

Sent from my iPad

On Jul 19, 2016, at 6:00 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

On your page, students make several choices to set up a problem. It appears 
that each choice does a GET and reloads the page from sever with appropriate 
page modification. How hard would it be to return the correct SMILES on each of 
these GETS?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 4:35 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
Other information in the database includes:  CAS RN, InChI, InChiKey, and 
ChemSpider ID.  I’m aware that the different sources for SMILES is a potential 
issue, having already dealt with that.  I’m also aware that compounds can have 
more than one CAS number and more than one ChemSpider ID even though I learned 
that CAS numbers were unique b

Re: [Jmol-users] JSME and SMILES

2016-07-20 Thread Jennifer L. Muzyka

Otis,
There are several possible different answer SMILES because there are several 
different possible starting materials that would give the same product, at 
least for most combinations of reagent and product.  I suspect that’s not a 
real issue with Jmol, but that’s why I started going back to query the database 
again.

The student who imported the additional 3800 compounds into the database was in 
the fall 2015 OLCC cheminformatics class.  I’m confident he used PubChem or 
other cheminformatics tools to build the table associated with the new 
compounds, although that wasn’t his project for the course.  It was something 
he did for fun, as he continues to develop the app for which he (and a buddy) 
won the prize in the NIST competition last fall.  He’s since graduated.  I’ll 
be there for the OLCC retreat before the BCCE and expect to offer the OLCC 
course again on Centre’s campus in spring 2017.
Jennifer








On Jul 19, 2016, at 8:58 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

The student SMILES and the answer SMILES need to be compared on the client 
(browser) side via JavaScript. The student answer SMILES is already on the 
client side. All we would need is the answer SMILES there also.

Having said this, I know that Bob H once mentioned running the Java app on the 
server to do server side tasks, but running the Java app on the server is way 
beyond my programming skills.

With the power of modern JavaScript and HTML5, I’m not sure I see why the 
computer jocks are more comfortable with a second hit on the server. The fact 
is that the server cannot do the SMILES comparison as elegantly as Bob’s JSmol 
SMILES comparison, that is unless the Jmol Java App is run on the server. With 
the client side JavaScript/HTML5 power, it seems to me going back to the server 
is just going back to the server in order to go back to the server!

All of this, of course, is dependent on getting the answer SMILES into the 
working webpage.

Whichever route you go, that still leaves you with a database with some SMILES 
issues. Here’s a suggestion: How soon is Bob B’s cheminformatics course going 
into action again? Reconstructing your database entirely from Resolver (maybe 
PubChem) by an automated process would be a great real world project for one of 
the student teams. ( cc to Bob B)

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org

On Jul 19, 2016, at 8:22 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
What you are describing is essentially how I handle the code for the page where 
students draw the product structure.  It's certainly doable for the starting 
material structure as well.  I would just need to work out the different query 
and JavaScript.  My computer science colleagues would probably consider that 
the brute force method, unlike the more elegant Ajax method that goes back and 
queries the database a second time.  Is there some advantage to keeping all of 
the code within the page rather than going back to the database?  Those use PHP 
and MySQL.
Jennifer

Sent from my iPad

On Jul 19, 2016, at 6:00 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

On your page, students make several choices to set up a problem. It appears 
that each choice does a GET and reloads the page from sever with appropriate 
page modification. How hard would it be to return the correct SMILES on each of 
these GETS?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 4:35 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
Other information in the database includes:  CAS RN, InChI, InChiKey, and 
ChemSpider ID.  I’m aware that the different sources for SMILES is a potential 
issue, having already dealt with that.  I’m also aware that compounds can have 
more than one CAS number and more than one ChemSpider ID even though I learned 
that CAS numbers were unique back when I was in college.  An unfortunate 
reality is that I don’t have all of the keys for every compound.  Another 
potential problem with the database is that I might not have removed all of the 
situations where a single compound appeared more than once.  There are other 
things in the database (gifs, pdbs, jcamp spectra) for some compounds.
Jennifer





On Jul 19, 2016, at 4:22 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

The default is that JSME keeps explicit hydrogens to carbon, and these will 
show up in brackets. An option can be used to turn this off.

It sounds like you have a mix of SMILES that may have been created by options 
variations in the JSME implementations being used. That's a problem.

One

Re: [Jmol-users] JSME and SMILES

Otis,
What you are describing is essentially how I handle the code for the page where 
students draw the product structure.  It's certainly doable for the starting 
material structure as well.  I would just need to work out the different query 
and JavaScript.  My computer science colleagues would probably consider that 
the brute force method, unlike the more elegant Ajax method that goes back and 
queries the database a second time.  Is there some advantage to keeping all of 
the code within the page rather than going back to the database?  Those use PHP 
and MySQL.
Jennifer

Sent from my iPad

On Jul 19, 2016, at 6:00 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

On your page, students make several choices to set up a problem. It appears 
that each choice does a GET and reloads the page from sever with appropriate 
page modification. How hard would it be to return the correct SMILES on each of 
these GETS?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org

On Jul 19, 2016, at 4:35 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
Other information in the database includes:  CAS RN, InChI, InChiKey, and 
ChemSpider ID.  I’m aware that the different sources for SMILES is a potential 
issue, having already dealt with that.  I’m also aware that compounds can have 
more than one CAS number and more than one ChemSpider ID even though I learned 
that CAS numbers were unique back when I was in college.  An unfortunate 
reality is that I don’t have all of the keys for every compound.  Another 
potential problem with the database is that I might not have removed all of the 
situations where a single compound appeared more than once.  There are other 
things in the database (gifs, pdbs, jcamp spectra) for some compounds.
Jennifer





On Jul 19, 2016, at 4:22 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

The default is that JSME keeps explicit hydrogens to carbon, and these will 
show up in brackets. An option can be used to turn this off.

It sounds like you have a mix of SMILES that may have been created by options 
variations in the JSME implementations being used. That's a problem.

One more question, and then I'll do some more thinking. What other items or 
keys are in the database?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 4:01 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
1200 of the compounds have SMILES that agree with the JSME version.  Those were 
generated by a buddy of mine.  Then when I found some disagreed, I went through 
them one by one to fix the ones that disagree.

The next 3800 came from some other source than JSME when one of my students 
imported the compounds into the database.  Most of those are not involved in 
reactions so those compounds might not be relevant.  I anticipate that I would 
change them one by one if needed so that they agree with JSME.  None of those 
have SMILES that look like the stuff with brackets and H’s that JSME produces.  
They tend to use the slashes to indicate double bond stereochemistry and @ to 
indicate chirality at stereocenters.  (People who are more proficient 
programmers than I am could probably complete the task more rapidly by 
automating it.)

Now I’m adding new reactions to accompany the question type where students draw 
the starting material rather than the product, I’m adding new compounds one by 
one.  I’m getting the SMILES for each of those compounds from the JSME database.
Jennifer



On Jul 19, 2016, at 3:51 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

On the student side, Jmol and JSME would be working together. This is no big 
deal - very easy. The problem is server side.

Let me think about this. Some important points: Do your existing database 
SMILES have stereo chemistry - i.e. / \ and @ notation where appropriate? Are 
they all JSME SMILES? Is there a possibility that the database creators may 
have drawn explicit hydrogens on carbon in non-stereo contect?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 3:37 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
The SMILES database has about 5000 compounds in it.  I’m  confused about how 
JSmol works here.  Would there be a JSmol drawing interface rather than JSME?  
I guess I need to go read the Jmol documentation about how to get the SMILES 
stuff working.  Is there some automated process to get the Jmol versions of the 
SMILES to update the database?
Jennifer




On Jul 19, 2

Re: [Jmol-users] JSME and SMILES

Otis,
Other information in the database includes:  CAS RN, InChI, InChiKey, and 
ChemSpider ID.  I’m aware that the different sources for SMILES is a potential 
issue, having already dealt with that.  I’m also aware that compounds can have 
more than one CAS number and more than one ChemSpider ID even though I learned 
that CAS numbers were unique back when I was in college.  An unfortunate 
reality is that I don’t have all of the keys for every compound.  Another 
potential problem with the database is that I might not have removed all of the 
situations where a single compound appeared more than once.  There are other 
things in the database (gifs, pdbs, jcamp spectra) for some compounds.
Jennifer





On Jul 19, 2016, at 4:22 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

The default is that JSME keeps explicit hydrogens to carbon, and these will 
show up in brackets. An option can be used to turn this off.

It sounds like you have a mix of SMILES that may have been created by options 
variations in the JSME implementations being used. That's a problem.

One more question, and then I'll do some more thinking. What other items or 
keys are in the database?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 4:01 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
1200 of the compounds have SMILES that agree with the JSME version.  Those were 
generated by a buddy of mine.  Then when I found some disagreed, I went through 
them one by one to fix the ones that disagree.

The next 3800 came from some other source than JSME when one of my students 
imported the compounds into the database.  Most of those are not involved in 
reactions so those compounds might not be relevant.  I anticipate that I would 
change them one by one if needed so that they agree with JSME.  None of those 
have SMILES that look like the stuff with brackets and H’s that JSME produces.  
They tend to use the slashes to indicate double bond stereochemistry and @ to 
indicate chirality at stereocenters.  (People who are more proficient 
programmers than I am could probably complete the task more rapidly by 
automating it.)

Now I’m adding new reactions to accompany the question type where students draw 
the starting material rather than the product, I’m adding new compounds one by 
one.  I’m getting the SMILES for each of those compounds from the JSME database.
Jennifer



On Jul 19, 2016, at 3:51 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

On the student side, Jmol and JSME would be working together. This is no big 
deal - very easy. The problem is server side.

Let me think about this. Some important points: Do your existing database 
SMILES have stereo chemistry - i.e. / \ and @ notation where appropriate? Are 
they all JSME SMILES? Is there a possibility that the database creators may 
have drawn explicit hydrogens on carbon in non-stereo contect?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 3:37 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
The SMILES database has about 5000 compounds in it.  I’m  confused about how 
JSmol works here.  Would there be a JSmol drawing interface rather than JSME?  
I guess I need to go read the Jmol documentation about how to get the SMILES 
stuff working.  Is there some automated process to get the Jmol versions of the 
SMILES to update the database?
Jennifer




On Jul 19, 2016, at 2:00 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

For the most part,  there is no cross application canonical SMILES. Daylight 
never released the technical details to their reduction to canonical algorithm. 
Consequently, uniqueness exists only within a given “copycat” application. I 
believe PubChem uses Open Eye SMILES. If you were comparing Open Eye unique 
SMILES to Open Eye unique SMILE, you could do a simple string comparison.

JSME is top notch in my opinion. I would not use any other online drawing 
software, but with JSME, you cannot have canonical (unique) SMILES AND 
stereochemistry. If you want simple string comparison, both SMILES (sever and 
student drawn) will have to be JSME without E/Z and stereo chemistry. I’m 
almost certain that this has not changed since the "old doc" in the previous 
email. I think this means that you are going to have to use these explicit 
options in server and client JSME SMILE creation: noquery (this is default), 
noautoez, canonize (this is default), nostereo. I’d list all explicitly.

This probably not what you actually want, and that’s the absolute beauty of 
what Bob crea

Re: [Jmol-users] JSME and SMILES

Otis,
1200 of the compounds have SMILES that agree with the JSME version.  Those were 
generated by a buddy of mine.  Then when I found some disagreed, I went through 
them one by one to fix the ones that disagree.

The next 3800 came from some other source than JSME when one of my students 
imported the compounds into the database.  Most of those are not involved in 
reactions so those compounds might not be relevant.  I anticipate that I would 
change them one by one if needed so that they agree with JSME.  None of those 
have SMILES that look like the stuff with brackets and H’s that JSME produces.  
They tend to use the slashes to indicate double bond stereochemistry and @ to 
indicate chirality at stereocenters.  (People who are more proficient 
programmers than I am could probably complete the task more rapidly by 
automating it.)

Now I’m adding new reactions to accompany the question type where students draw 
the starting material rather than the product, I’m adding new compounds one by 
one.  I’m getting the SMILES for each of those compounds from the JSME database.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jul 19, 2016, at 3:51 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

On the student side, Jmol and JSME would be working together. This is no big 
deal - very easy. The problem is server side.

Let me think about this. Some important points: Do your existing database 
SMILES have stereo chemistry - i.e. / \ and @ notation where appropriate? Are 
they all JSME SMILES? Is there a possibility that the database creators may 
have drawn explicit hydrogens on carbon in non-stereo contect?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 3:37 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
The SMILES database has about 5000 compounds in it.  I’m  confused about how 
JSmol works here.  Would there be a JSmol drawing interface rather than JSME?  
I guess I need to go read the Jmol documentation about how to get the SMILES 
stuff working.  Is there some automated process to get the Jmol versions of the 
SMILES to update the database?
Jennifer




On Jul 19, 2016, at 2:00 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

For the most part,  there is no cross application canonical SMILES. Daylight 
never released the technical details to their reduction to canonical algorithm. 
Consequently, uniqueness exists only within a given “copycat” application. I 
believe PubChem uses Open Eye SMILES. If you were comparing Open Eye unique 
SMILES to Open Eye unique SMILE, you could do a simple string comparison.

JSME is top notch in my opinion. I would not use any other online drawing 
software, but with JSME, you cannot have canonical (unique) SMILES AND 
stereochemistry. If you want simple string comparison, both SMILES (sever and 
student drawn) will have to be JSME without E/Z and stereo chemistry. I’m 
almost certain that this has not changed since the "old doc" in the previous 
email. I think this means that you are going to have to use these explicit 
options in server and client JSME SMILE creation: noquery (this is default), 
noautoez, canonize (this is default), nostereo. I’d list all explicitly.

This probably not what you actually want, and that’s the absolute beauty of 
what Bob created in JSmol! With Bob’s approach, the cross application unique 
SMILES barriers do not matter. Bob took the expression “unique SMILES” and made 
it obsolete!

To do this (include stereochemistry via Bob’s approach) you will also have to 
make some options selections in JSME, but you will also be able to use E/Z and 
stereochemistry.

How large is your SMILES database?

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 19, 2016, at 1:23 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
The SMILES goes back to the MySQL database for comparison rather than just 
running JavaScript within the browser.  The stuff in the database was all 
generated with JSME.  (So I’m confused about how adding Jmol to the mix will 
help.)  The “canonical” SMILES generated by JSME sure doesn’t look like the 
canonical SMILES provided in PubChem.  But maybe I’m actually getting SMARTS?  
I will go read the documentation you have pointed out.
Jennifer






On Jul 18, 2016, at 10:56 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>

Re: [Jmol-users] JSME and SMILES

Otis,
The SMILES database has about 5000 compounds in it.  I’m  confused about how 
JSmol works here.  Would there be a JSmol drawing interface rather than JSME?  
I guess I need to go read the Jmol documentation about how to get the SMILES 
stuff working.  Is there some automated process to get the Jmol versions of the 
SMILES to update the database?
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jul 19, 2016, at 2:00 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

For the most part,  there is no cross application canonical SMILES. Daylight 
never released the technical details to their reduction to canonical algorithm. 
Consequently, uniqueness exists only within a given “copycat” application. I 
believe PubChem uses Open Eye SMILES. If you were comparing Open Eye unique 
SMILES to Open Eye unique SMILE, you could do a simple string comparison.

JSME is top notch in my opinion. I would not use any other online drawing 
software, but with JSME, you cannot have canonical (unique) SMILES AND 
stereochemistry. If you want simple string comparison, both SMILES (sever and 
student drawn) will have to be JSME without E/Z and stereo chemistry. I’m 
almost certain that this has not changed since the "old doc" in the previous 
email. I think this means that you are going to have to use these explicit 
options in server and client JSME SMILE creation: noquery (this is default), 
noautoez, canonize (this is default), nostereo. I’d list all explicitly.

This probably not what you actually want, and that’s the absolute beauty of 
what Bob created in JSmol! With Bob’s approach, the cross application unique 
SMILES barriers do not matter. Bob took the expression “unique SMILES” and made 
it obsolete!

To do this (include stereochemistry via Bob’s approach) you will also have to 
make some options selections in JSME, but you will also be able to use E/Z and 
stereochemistry.

How large is your SMILES database?

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org

On Jul 19, 2016, at 1:23 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Otis,
The SMILES goes back to the MySQL database for comparison rather than just 
running JavaScript within the browser.  The stuff in the database was all 
generated with JSME.  (So I’m confused about how adding Jmol to the mix will 
help.)  The “canonical” SMILES generated by JSME sure doesn’t look like the 
canonical SMILES provided in PubChem.  But maybe I’m actually getting SMARTS?  
I will go read the documentation you have pointed out.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org<http://organicers.org/>

859-238-5413
fax 859-236-7925






On Jul 18, 2016, at 10:56 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

I knew this statement was out there. It took me a while to find the Web doc:

"public String JME.smiles()

returns a SMILES string of the current molecule(s) or reaction. For single 
molecule without stereochemistry the SMILES is unique, unification is not yet 
implemented for molecules with stereochemistry and for reactions.”
http://www.molinspiration.com/jme/doc/jme_functions.html

It’s an old doc, but I’m sure it still applies.

Since canonize is the default in JSME, you’re going to have to select 
nocanonize!

Also, your current option setting sets the “query” option. That sets up SMARTS 
mode. I don’t think that is what you want?

Although it’s commented out in your current HTML, it looks like you are set of 
for a simple string comparison. That’s not going to work. This is where Bob’s 
JSmol .find approach comes into play - my previous email.

I’ve been using a Jmol/JSME SMILES comparison for quite a while, so don’t 
hesitate to ask if you need more specific information.

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jul 18, 2016, at 4:22 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

You have to set SMILES settings in the JSME options part of your JSME set-up to 
invoke stereochemistry and E/Z. This page explains all of the options and the 
set up procedure:

http://peter-ertl.com/jsme/JSME_2015-06-14/doc.html

BUT, BUT,  it looks like you are doing SMILES comparisons, and with 
stereochemistry and E/Z invoked, I’m

Re: [Jmol-users] JSME and SMILES

Otis,
The SMILES goes back to the MySQL database for comparison rather than just 
running JavaScript within the browser.  The stuff in the database was all 
generated with JSME.  (So I’m confused about how adding Jmol to the mix will 
help.)  The “canonical” SMILES generated by JSME sure doesn’t look like the 
canonical SMILES provided in PubChem.  But maybe I’m actually getting SMARTS?  
I will go read the documentation you have pointed out.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jul 18, 2016, at 10:56 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

I knew this statement was out there. It took me a while to find the Web doc:

"public String JME.smiles()

returns a SMILES string of the current molecule(s) or reaction. For single 
molecule without stereochemistry the SMILES is unique, unification is not yet 
implemented for molecules with stereochemistry and for reactions.”
http://www.molinspiration.com/jme/doc/jme_functions.html

It’s an old doc, but I’m sure it still applies.

Since canonize is the default in JSME, you’re going to have to select 
nocanonize!

Also, your current option setting sets the “query” option. That sets up SMARTS 
mode. I don’t think that is what you want?

Although it’s commented out in your current HTML, it looks like you are set of 
for a simple string comparison. That’s not going to work. This is where Bob’s 
JSmol .find approach comes into play - my previous email.

I’ve been using a Jmol/JSME SMILES comparison for quite a while, so don’t 
hesitate to ask if you need more specific information.

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org

On Jul 18, 2016, at 4:22 PM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

You have to set SMILES settings in the JSME options part of your JSME set-up to 
invoke stereochemistry and E/Z. This page explains all of the options and the 
set up procedure:

http://peter-ertl.com/jsme/JSME_2015-06-14/doc.html

BUT, BUT,  it looks like you are doing SMILES comparisons, and with 
stereochemistry and E/Z invoked, I’m pretty sure JSME SMILES are not unique. 
The best way to compare SMILES is with JSmol. In the case of your page, you 
could hide JSmol on the page. Comparison can be done in JavaScript:

function compSmiles(key, ans) {
key = key.replace(/\\/g, '');
ans = ans.replace(/\\/g, '');
return Jmol.evaluateVar(jmolApplet0. "'" + key + "'.find('SMILES','" + ans + 
"') > 0");
}

My quotes above are hard to read, so here’s the function with spaces to 
emphasis the quotes:

function compSmiles(key, ans) {
key = key.replace(/\\/g, '  ');
ans = ans.replace(/\\/g, '  ');
return Jmol.evaluateVar(jmolApplet0. " ' " + key + " '.find('SMILES',' " + ans 
+ " ') > 0");
}

The replace statements above are needed to place the SMILES \ notation into a 
JavaScript string - i.e. correct the fact that \ in a character escape in 
JavaScript.

Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org

On Jul 18, 2016, at 3:39 PM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

I’m not sure if this listserv is the proper place for me to ask this question, 
but I’m not sure where else to ask.  I’m using the JSME embedded within 
Jmol/JSmol to let students practice reaction questions where they can draw 
products.  The ability to draw starting materials is currently in development.  
My problem is that JSME generates some quirky SMILES strings.  Cis and 
trans-3-hexene both generate [H]C(CC)=C([H])CC, so it’s not possible to 
distinguish the stereoisomers.  If I don’t draw in the stereochemistry 
explicitly, I get the canonical SMILES.  (If you’d like to see the page in 
development, feel free to check it out at 
http://chemserv.centre.edu/muzyka/reactionzoo/jsmol/jsme/JSMEreaction17.php)

The documentation for JSME says it generates canonical SMILES, but I haven’t 
seen any other SMILES that use the brackets with the H atoms.

If you guys can point me to an alternate location to ask this question, I’d 
appreciate it.
Thanks







--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2

[Jmol-users] JSME and SMILES

2016-07-18 Thread Jennifer L. Muzyka

I’m not sure if this listserv is the proper place for me to ask this question, 
but I’m not sure where else to ask.  I’m using the JSME embedded within 
Jmol/JSmol to let students practice reaction questions where they can draw 
products.  The ability to draw starting materials is currently in development.  
My problem is that JSME generates some quirky SMILES strings.  Cis and 
trans-3-hexene both generate [H]C(CC)=C([H])CC, so it’s not possible to 
distinguish the stereoisomers.  If I don’t draw in the stereochemistry 
explicitly, I get the canonical SMILES.  (If you’d like to see the page in 
development, feel free to check it out at 
http://chemserv.centre.edu/muzyka/reactionzoo/jsmol/jsme/JSMEreaction17.php)

The documentation for JSME says it generates canonical SMILES, but I haven’t 
seen any other SMILES that use the brackets with the H atoms.

If you guys can point me to an alternate location to ask this question, I’d 
appreciate it.
Thanks




Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] updating SpectralZoo problems

2016-06-15 Thread Jennifer L. Muzyka

Otis,
I’m not using GoDaddy.  My stuff is all hosted at Centre College.  The 
SpectralZoo and ReactionZoo are on a server by themselves, so sometimes weird 
stuff happens to that server and ITS is less likely to find out about it 
because most it’s off the beaten path.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jun 13, 2016, at 10:59 AM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Jennifer,

The page hangs for me on the first structure load, BUT if I wait it out, all is 
OK. I missed this point in my initial check. All is well after this initial 
load.

This initial hang, however, is repeated in some subsequent (no cache clearing) 
new sessions. I don’t know that this is a problem, but it mirrors a behavior 
that I’m seeing on my site now that I moved to GoDaddy. Since it’s not related 
to local cache, I’ve been assuming that its related to the GoDaddy Name Server 
DNS software. It’s irritating, but there’s not much I can do about it. I’m 
spoiled because my site was on a high end service that I had to drop because of 
cost/space limitations.

So I think I’m seeing this type of Name Server DNS software delay on your 
page’s initial load on occasion. I just did not catch it at fist because I was 
thinking that the page was already loaded. It was, but that load structure 
button is loading a new page!

Are you using GoDaddy by any chance?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org

On Jun 13, 2016, at 10:18 AM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Hi Jennifer,

I hate to be a "poop," but even with cache clearing this page is still not 
working for me on Safari or Windows 10 Edge:

http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/specZoo.php

Is this the page that you were referencing in your latest note?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
mistake.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org<http://organicers.org/>

859-238-5413
fax 859-236-7925






On Jun 11, 2016, at 6:08 AM, Angel Herráez 
<angel.herr...@uah.es<mailto:angel.herr...@uah.es>> wrote:

Jennifer,

Your page

http://chemserv.centre.edu/muzyka/spectralzoo

is mostly functional for me (at least in Firefox Windows7).

1. JSpecViewer loads, and it loads spectra when I click on the buttons.

2. JSmol aldo loads, althoug it is hidden due to the css rule
  #structure { display: none; }

3. The [Show Structure] button is not working because it sends data to a 
structure.htm page that does not exist. I have made a local duplicate of your 
page with the proper structure.htm file and it also works.


So I believe there is no problem due to upgrading your JSmol version, there is 
no JmolScript problem, even Javascript problems.
You have most likely a mixed up collection of pieces of javascript code 
inherited from previous page.

For example,
- you are calling jquery.js twice (at the top and the bottom of your page) -- 
in fact, three times counting the copy included in JSmol.min.js
- you are calling a mixture of JSmol-related js files, which are not needed as 
Otis pointed out
- you are missing or have the wrong path to structure.htm

This is my advice:

(head section) Leave just these:





(bottom of body) Remove this line:

 

Optionally:

You can probably remove the jmol_isReady  part, and clean up your Info 
definitions to these:

Info = {
  width: 800,
  height: 300,
  color: "#FF",
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
  disableInitialConsole: true,
  use: "HTML5"
}
var Info2 = {
  width: 200,
  height: 200,
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
  use: "HTML5",
  j2sPath: "j2s"
}

Although not important for your setup, this is the correct function, just in 
case:

function cloneJSmol(JSmolObject) {
  var t = JSmolObject._jmolType; //temp
  if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
  else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
  else if ( /_Applet/.test(t) ) { t = 'Jav

Re: [Jmol-users] updating SpectralZoo pages

2016-06-13 Thread Jennifer L. Muzyka

It is working for me.  It was a cache problem, like Angel and you both 
suggested.

Jennifer



Jennifer Muzyka
H. W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka

From: Robert Hanson 
Sent: Monday, June 13, 2016 8:44 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] updating SpectralZoo pages

Looks good now. Working for you, Jennifer??

Bob
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Jennifer L. Muzyka

Otis,
That IS the page I was referring to.  I’m happy to have you testing it for me 
on different platforms - I don’t have access to Windows 10 Edge.  What kind of 
errors to you see?

I do have access to Safari, and it works on my Mac running Yosemite.  I haven’t 
tested with mobile Safari.  Please tell me more about what you see so that I 
can address the problems, Otis.
Jennifer








Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jun 13, 2016, at 10:18 AM, Otis Rothenberger 
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:

Hi Jennifer,

I hate to be a "poop," but even with cache clearing this page is still not 
working for me on Safari or Windows 10 Edge:

http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/specZoo.php

Is this the page that you were referencing in your latest note?

Otis

--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>

On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka 
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:

Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
mistake.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org<http://organicers.org/>

859-238-5413
fax 859-236-7925






On Jun 11, 2016, at 6:08 AM, Angel Herráez 
<angel.herr...@uah.es<mailto:angel.herr...@uah.es>> wrote:

Jennifer,

Your page

http://chemserv.centre.edu/muzyka/spectralzoo

is mostly functional for me (at least in Firefox Windows7).

1. JSpecViewer loads, and it loads spectra when I click on the buttons.

2. JSmol aldo loads, althoug it is hidden due to the css rule
  #structure { display: none; }

3. The [Show Structure] button is not working because it sends data to a 
structure.htm page that does not exist. I have made a local duplicate of your 
page with the proper structure.htm file and it also works.


So I believe there is no problem due to upgrading your JSmol version, there is 
no JmolScript problem, even Javascript problems.
You have most likely a mixed up collection of pieces of javascript code 
inherited from previous page.

For example,
- you are calling jquery.js twice (at the top and the bottom of your page) -- 
in fact, three times counting the copy included in JSmol.min.js
- you are calling a mixture of JSmol-related js files, which are not needed as 
Otis pointed out
- you are missing or have the wrong path to structure.htm

This is my advice:

(head section) Leave just these:





(bottom of body) Remove this line:

 

Optionally:

You can probably remove the jmol_isReady  part, and clean up your Info 
definitions to these:

Info = {
  width: 800,
  height: 300,
  color: "#FF",
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
  disableInitialConsole: true,
  use: "HTML5"
}
var Info2 = {
  width: 200,
  height: 200,
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
  use: "HTML5",
  j2sPath: "j2s"
}

Although not important for your setup, this is the correct function, just in 
case:

function cloneJSmol(JSmolObject) {
  var t = JSmolObject._jmolType; //temp
  if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
  else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
  else if ( /_Applet/.test(t) ) { t = 'Java'; }
  else { t = null; }
  JSmolCloneData.type = t;
  JSmolCloneData.state = Jmol.getPropertyAsString(JSmolObject, 'stateInfo');
  window.open(' structure.htm','JSmolPopup','resizable, width=500, height=500');
}



--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. 
https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and

Re: [Jmol-users] updating SpectralZoo problems

2016-06-13 Thread Jennifer L. Muzyka

Thanks for Angel and Otis for helping me with the troubleshooting.  After I 
cleared my cache, it works for me too!  I’m embarrassed to make such a silly 
mistake.
Jennifer






Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Jun 11, 2016, at 6:08 AM, Angel Herráez 
> wrote:

Jennifer,

Your page

http://chemserv.centre.edu/muzyka/spectralzoo

is mostly functional for me (at least in Firefox Windows7).

1. JSpecViewer loads, and it loads spectra when I click on the buttons.

2. JSmol aldo loads, althoug it is hidden due to the css rule
  #structure { display: none; }

3. The [Show Structure] button is not working because it sends data to a 
structure.htm page that does not exist. I have made a local duplicate of your 
page with the proper structure.htm file and it also works.


So I believe there is no problem due to upgrading your JSmol version, there is 
no JmolScript problem, even Javascript problems.
You have most likely a mixed up collection of pieces of javascript code 
inherited from previous page.

For example,
- you are calling jquery.js twice (at the top and the bottom of your page) -- 
in fact, three times counting the copy included in JSmol.min.js
- you are calling a mixture of JSmol-related js files, which are not needed as 
Otis pointed out
- you are missing or have the wrong path to structure.htm

This is my advice:

(head section) Leave just these:





(bottom of body) Remove this line:

 

Optionally:

You can probably remove the jmol_isReady  part, and clean up your Info 
definitions to these:

Info = {
  width: 800,
  height: 300,
  color: "#FF",
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
  disableInitialConsole: true,
  use: "HTML5"
}
var Info2 = {
  width: 200,
  height: 200,
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
  use: "HTML5",
  j2sPath: "j2s"
}

Although not important for your setup, this is the correct function, just in 
case:

function cloneJSmol(JSmolObject) {
  var t = JSmolObject._jmolType; //temp
  if ( /_Canvas2D/.test(t) ) { t = 'HTML5'; }
  else if ( /_Canvas3D/.test(t) ) { t = 'WebGL'; }
  else if ( /_Applet/.test(t) ) { t = 'Java'; }
  else { t = null; }
  JSmolCloneData.type = t;
  JSmolCloneData.state = Jmol.getPropertyAsString(JSmolObject, 'stateInfo');
  window.open(' structure.htm','JSmolPopup','resizable, width=500, height=500');
}



--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. 
https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] updating SpectralZoo problems

2016-06-10 Thread Jennifer L. Muzyka

Thanks to Eric and Otis and others who have offered suggestions.  I am coming 
to believe that something is indeed wrong with my installation.  Yesterday I 
downloaded the zip file from Sourceforge.  Then I copied the jsmol folder to 
the server.  When I try to open the example files 
(http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/supersimple.htm) I see the 
same error messages that I sometimes see with the SpectralZoo file -
[Java2Script] The required class file

j2s/J/c/ANIM.js
could not be loaded. Script error: expected expression, got '<'

data:



404 Not Found

Not Found
The requested URL /muzyka/spectralzoo/jsmol/j2s/J/c/ANIM.js was not found on 
this server.

Apache/2.4.7 (Ubuntu) Server at 
chemserv.centre.edu Port 80


Sure enough, there’s no file name ANIM.js in the c folder.  Is there something 
wrong with my approach to copy the whole directory over?
Any advice?
Jennifer




Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] updating SpectralZoo pages

2016-06-09 Thread Jennifer L. Muzyka

We recently got a new server to host the SpectralZoo 
(http://chemserv.centre.edu/muzyka/spectralzoo), with new versions of PHP and 
MySQL.  Some of my SpectralZoo scripts broke, so I thought it might be time to 
upgrade the Jmol (actually JSmol) that I’m using on the site.  I see even more 
errors, and I’m stumped about how to solve them.  It looks like I was 
previously using a version of Jmol from 11/2013.  Can someone point me to 
something to read to help me sort out the changes so that I can manage the 
troubleshooting?  (Clearly I have been away from programming for too long…..)  
I would appreciate any advice you can offer or articles you can point me 
towards.  Thanks.
Jennifer








Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] isosurface functionally JSmol

2015-08-05 Thread Jennifer L. Muzyka

Is it possible to display an isosurface from a function (xy or xyz) in JSmol?  
When I try to do this with scripts from Jmol example pages, it crashes 
JavaScript.  Those example pages might be from old versions of Jmol (11 or 12). 
 So maybe this capability is no longer supported?
Jennifer



Jennifer Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






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

[Jmol-users] JSV -trouble with integration options

2014-09-23 Thread Jennifer L. Muzyka

When my students are using IE on their spectra, they are unable to modify their 
integrals.  The problem happens on multiple computers.  I think all computers 
were running Win7.  These problems are observed at 
http://chemserv.centre.edu/listing3.php?cat=nmr
I tell the students to use a different browser and things seem okay.  Should it 
work with IE?
-Jennifer


Jennifer Muzyka
Professor of Chemistry
Centre College
600 W. Walnut St.
Danville, KY. 40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
--
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] JspecView file path

2014-08-25 Thread Jennifer L. Muzyka

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

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





Jennifer Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edumailto:jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925





--
Slashdot TV.  
Video for Nerds.  Stuff that matters.
http://tv.slashdot.org/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] JSV in web app

2014-07-15 Thread Jennifer L. Muzyka

I am finally getting around to trying to put the JavaScript version of 
JSpecView into the Spectral Zoo so that I can get away from using Java.  I 
started with the testjsv.htm page, as it seems to be the simplest one in the 
most recent download.  I would like to have a spectrum displayed without a 
search box and without most of the options that show up at the bottom of this 
page.  I don't see those items in the body of the html page when I try to edit 
it, which leads me to believe they are generated by the code that displays the 
applet.  Can somebody point me to a resource that will describe how I control 
the options that hide or show the box that allows me to query databases?  That 
unnecessary option is likely to confuse users of my app.  Thanks.
Jennifer



Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] WebMO

2013-02-22 Thread Jennifer L. Muzyka

Does anybody know about a JSmol version of WebMO?  We're going to have trouble 
doing computational chemistry experiments in our teaching labs without Java, 
since we use WebMO.  I would appreciate any information or insights anybody can 
offer.  Thanks.
Jennifer





Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] WebMO

2013-02-22 Thread Jennifer L. Muzyka

Bob,
Java has been disabled on all campus computers at Centre.  I think Centre's 
response is pretty reasonable, given that Homeland Security recommends 
disabling Java.  See the article the ITS folks shared with me:  
http://www.informationweek.com/security/vulnerabilities/10-facts-secure-java-for-business-use/240146322

http://www.informationweek.com/security/vulnerabilities/10-facts-secure-java-for-business-use/240146322
In addition to Centre and Homeland Security, many of the browser manufacturers 
are disabling Java so users don't have much choice.  I think Apple has done 
that with Safari (which I don't use).  I'm especially thrilled about the 
existence of JSmol.  It's very timely.
Jennifer




On Feb 22, 2013, at 2:51 PM, 
jmol-users-requ...@lists.sourceforge.netmailto:jmol-users-requ...@lists.sourceforge.net
 wrote:

--

Message: 1
Date: Fri, 22 Feb 2013 13:16:17 -0600
From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu
Subject: Re: [Jmol-users] WebMO
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Message-ID:
caf_yuvutvpukm1sseq12w3kt2sg1fs6mn-pwbcljnawo2di...@mail.gmail.commailto:caf_yuvutvpukm1sseq12w3kt2sg1fs6mn-pwbcljnawo2di...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1

No sign of that yet.

Is there a reason you do not have Java in your teaching labs? Is this just
an IT department crack-down? St. Olaf is still supporting Java


On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka 
jennifer.muz...@centre.edumailto:jennifer.muz...@centre.edu wrote:

Does anybody know about a JSmol version of WebMO?  We're going to have
trouble doing computational chemistry experiments in our teaching labs
without Java, since we use WebMO.  I would appreciate any information or
insights anybody can offer.  Thanks.
Jennifer





Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edumailto:jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] WebMO

2013-02-22 Thread Jennifer L. Muzyka

Mike,
Thanks for checking on the latest WebMO update.  I contacted them and they say 
there's no way all that complex Java stuff can be done with JavaScript.  On my 
reply, I copied Bob Hanson.  He responded with details about JSmol that will 
hopefully get the WebMO folks thinking about the topic.  In the meantime, maybe 
we can get ITS to let us use a little bit of Java on campus.

Centre's campus has changed a bit since you were here in 2003.  Let me know if 
you are here on campus and would like a tour of the chemistry facilities.
Jennifer



On Feb 22, 2013, at 1:14 PM, jmol-users-requ...@lists.sourceforge.net wrote:
 
 --
 
 Message: 3
 Date: Fri, 22 Feb 2013 12:14:33 -0600
 From: Michael Evans evan...@illinois.edu
 Subject: Re: [Jmol-users] WebMO
 To: jmol-users@lists.sourceforge.net
   jmol-users@lists.sourceforge.net
 Message-ID:
   CAPVVrdZ6cpzYX-Kp-pKoAB6sE85AkF5MzmKnTJj=wbttwsn...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Jennifer,
 Looks like the last update to WebMO was in August 2012. Perhaps a version
 employing JSMol is in the works? Not sure. I don't see any reason why it
 shouldn't be possible...Jmol just reads the output of WebMO calculations;
 it doesn't do any of the calculations itself.
 
 BTW, I lived at Centre for the Governor's Scholars Program back in 2003.
 Hard to believe it's been ten years since then...I'm sure the campus is as
 beautiful as ever!
 
 Cheers, Mike
 
 
 ---
 Michael Evans
 Department of Chemistry
 University of Illinois, Urbana-Champaign
 
 
 On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka 
 jennifer.muz...@centre.edu wrote:
 
 Does anybody know about a JSmol version of WebMO?  We're going to have
 trouble doing computational chemistry experiments in our teaching labs
 without Java, since we use WebMO.  I would appreciate any information or
 insights anybody can offer.  Thanks.
 Jennifer
 
 
 
 
 
 Jennifer L. Muzyka
 Professor of Chemistry
 Centre College
 600 West Walnut Street
 Danville, KY  40422
 
 jennifer.muz...@centre.edu
 http://web.centre.edu/muzyka/
 
 
 
 **

Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] figured out my own layout question

2013-02-20 Thread Jennifer L. Muzyka

If you go visit those URLs I just gave in a previous post, you'll see I figured 
out the answer to my own question.  I'm excited to finally have a chance to 
learn to use JSmol.  Thanks for the JavaScript version of my favorite app, Bob 
and others who worked on this conversion.  I appreciate your efforts!
Jennifer








Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol / ChemDoodle test results

2012-04-12 Thread Jennifer L. Muzyka

It works on my iPad!  Amazes me - very cool!
Jennifer


Jennifer Muzyka
Professor of Chemistry
Centre College
Danville, KY. 40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka


 Message: 2
 Date: Thu, 12 Apr 2012 17:39:19 -0500
 From: Robert Hanson hans...@stolaf.edu
 Subject: Re: [Jmol-users] Jmol/ChemDoodle -- test1
 To: jmol-users@lists.sourceforge.net
 Message-ID:
caf_yuvw9wmdg_fql7o+-aamkgbou4qr7_uom3yphvrkkyvr...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Paul, first, check this out now:
 
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
 
 I'd say that was a productive day!
 
 This page is even more interesting. Pending Jmol user reports, it should
 pull up a twiddlable model on all platforms. It's working on my iPhone, my
 Windows laptop, and my MacBook. I can force it into ChemDoodle WebGL mode
 within Chrome; I can force it into ChemDoodle nonWebGL mode in Firefox,
 Chrome, and Safari. Default of Jmol is working on all non-Java-challenged
 platforms (I still can't force it into ChemDoodle for MSIE, but the default
 is to use Jmol anyway for that platform, of course. I don't know if Kevin
 can get ChemDoodle going on MSIE. Doesn't look like my version will, but it
 looks like a simple error that is probably trappable.)
 
 

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] dots and export to POV-ray

2011-01-11 Thread Jennifer L. Muzyka

I'm generating some very high resolution images to decorate a new addition to 
one of our science buildings and am having some strange behavior with dots.  
The biochemists wanted to show DNA with dots to give the viewer a feel for the 
real sizes of the atoms in addition to showing the connectivity with the balls 
and sticks.  When I export to POV-ray, the dots seem to be de-emphasized more 
the larger the final image is.  So when I get a really large image (10,000 x 
10,000), the dots all but disappear.  I'm wondering if there's any way to make 
the dot density higher or something so that they don't become invisible.  I 
don't see any settings that I can tweak to increase the dot density in the 
documentation, however.  I would appreciate any advice or suggestions anybody 
has to keep the dots from disappearing.  Thanks!
Jennifer






Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how to avoid them. Understand 
malware threats, the impact they can have on your business, and how you 
can protect your company and customers by using code signing.
http://p.sf.net/sfu/oracle-sfdevnl
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Making movies (A. Dijkman)

2008-12-09 Thread Jennifer L. Muzyka

I've used Chem3D and Spartan to make movies.  I liked Chem3D better because 
Spartan would sometimes change the xyz coordinates to yzx when I changed from 
one structure to the next.
-Jennifer





--

Message: 1
Date: Mon, 8 Dec 2008 22:39:45 +0100
From: A. Dijkman [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Making movies
To: jmol-users@lists.sourceforge.net
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1

 I'd rather look for an external way to build the multi-model file.

That's exactly what I'm looking for. I'd found the website of chemtube3d, but 
that's not what I can use in my lessons.

Anyone else with idea's to make movies?

Arjan
  - Original Message -
  From: Angel Herr?ez
  To: A. Dijkman ; jmol-users@lists.sourceforge.net
  Sent: Saturday, December 06, 2008 7:25 PM
  Subject: Re: [Jmol-users] Making movies


  Hello Arjan


   My question:
   I'd like to make a movie of an esterification where molecules/atoms of the 
reactants move to
   form the ester. I've been searching the net now for 2 days, but I cannot 
find any documentation
   on this. Maybe I'm searching in the wrong place, so I've turned to you. I 
downloaded a xyz-file
   and included it in this message, to give you an idea of my intentions.


   Is there a program to make these files or do I have to start understanding 
the script (yes, I know,
   that's probably a good idea anyway:-])


  Yes, the problem is building the multi-model file for your reaction, similar 
to the one you downloaded. But that's not a Jmol task. Jmol will just 
display-animate the model once you have it built. There is little you can learn 
from scripting, apart from the way to play the animation.
  I do not know of a program that you can use to build the model.




  In fact, the thing MAY be done using Jmol scripting, as it can move atoms 
around, but that's not trivial at all. I'd rather look for an external way to 
build the multi-model file.


  There are a few websites that have animated mechanisms of reaction. Maybe you 
can find yours already built there.


  Please check out sites at
  http://wiki.jmol.org/index.php/Websites_Using_Jmol


  I particularly suggest  ChemTube3D, by Nick Greeves. For example:
  
http://www.chemtube3d.com/Nucleophilic%20substitution%20at%20the%20carbonyl%20group%20-%20Acid-catalysed%20ester%20hydrolysis%20and%20transesterification.html


  Once you've got your model, you may come back to this list if you need help 
with playing the animation. I (we) will be glad to help you.


  Good luck!



--
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
The future of the web can't happen without you.  Join us at MIX09 to help
pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] jmol movie

2008-10-05 Thread Jennifer L. Muzyka

I had no trouble watching the Jmol movie on my computer, running Windows XP.
-Jennifer





Message: 2
Date: Wed, 1 Oct 2008 12:25:34 -0500
From: Robert Hanson [EMAIL PROTECTED]
Subject: [Jmol-users] jmol movie
To: jmol-users@lists.sourceforge.net
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1

Question: Can you watch this movie on your machine? If so, how's the
resolution?

http://www.stolaf.edu/people/hansonr/temp/rasraf.avi

It's supposed to be 145 frames of a molecular dynamics calculation. It was
created using the following Jmol script followed by running a program called
VideoMach:

function createFrame
 var fname = movie_+_frameID[-2][0] + .jpg
 write image 500 500 @fname
end function

function createMovie
 var nframes = {*}.model.max
 for (var i = 1; i = nframes; i = i + 1)
   frame @i
   createFrame
 end for
end function

createMovie


Bob


--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.


-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK  win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] volume of cavities inside proteins?

Bob-
You're right that that I'm having a lot of fun learning about proteins and 
ligands and calculations involving their interactions on my sabbatical.  I'm at 
the University of Kentucky College of Pharmacy working with Chang-Guo Zhan, a 
physical chemist.  The group does structure based drug design.

Thanks for the suggestions about navigating through the cavities as well as the 
description of how to make the pdb animations.  The animations sound easier 
than I had hoped, and the navigation through the cavities sounds like an 
interesting travel experience that I can't wait to try.
-Jennifer




-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK  win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] jmol demo on sourceforge

I just tried the demo on the jmol.sourceforge.net page, and I get a an error 
instead of the demo.  The error says:  java:security.AccessControlException.
-Jennifer




Jennifer Muzyka
Professor of Chemistry
On sabbatical at University of Kentucky College of Pharmacy
Centre College
Danville, KY  40422

[EMAIL PROTECTED]
http://web.centre.edu/muzyka

-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK  win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] jmol demo on sourceforge

Angel-
Thanks for the additional information about the protein cavities / isosurfaces.

I tried following your advice about clearing my Java cache in order to get the 
Jmol applet on the front page to work, but my browser keeps getting a Page Load 
Error for the jmol wiki.  I was having the same problem last week as well.  
Other websites work okay for me, so I can't figure out what the problem might 
be.  On the other hand, I went back to the demo and this time it loaded just 
fine!  (Last time it failed with both IE and Firefox..)
-Jennifer



Message: 10
Date: Wed, 01 Oct 2008 17:31:37 +0200
From: Angel Herraez [EMAIL PROTECTED]
Subject: Re: [Jmol-users] jmol demo on sourceforge
To: jmol-users@lists.sourceforge.net
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=US-ASCII

Hi Jennifer

Thanks for reporting this. However, I am seeing no problem.
Please,
1.- Clear your Java cache
(procedure described at
http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache

2. Clear your browser cache. Quit your browser and reopen it

3. Try the page. If the problem still persists, please report
details: your browser, OS and Java versions, and any
messages in the Java console.

I assume that you mean the Jmol applet in the front page, not in the
demo sections, right?





-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK  win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] jmol demo on sourceforge