from:"Otis Rothenberger"

Bob,

Sure, add it. It's a powerful resource.

I looked at Jmol.js jmolLoadAjax_STOLAF_RCSB(). I get it now. I didn't know 
you could do that.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Robert Hanson" 
Sent: Tuesday, March 15, 2011 3:54 PM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public 
Databases 

So, Otis, what I am wondering about is whether you would allow us to add

jmolLoadAjax_STOLAF_NIH

to Jmol.js. It would allow any applet (or knowledgeable user on any 
applet's page) to load any of the NIH models into Jmol directly, without 
need for the signed applet. You can try this yourself for the PDB. Just go 
to any page on the web that uses Jmol and a relatively recent (3 years?) 
version of Jmol.js, and enter on the URL line:

javascript:void(jmolLoadAjax_STOLAF_RCSB())

As I said, this hasn't been tested much with recent browsers. 

Bob
 

On Tue, Mar 15, 2011 at 6:30 AM, Robert Hanson  wrote:


Speaking of public databases, this might be a time to test the facility 
that has been in Jmol for quite some time -- the ability of the UNSIGNED 
applet to access remote files via a JavaScript interface. I don't think 
anyone has capitalized on this, but there is a St. Olaf server that is 
built into Jmol.js. 


jmolLoadAjax_STOLAF_RCSB


Could we adapt this, Otis, to get small molecules into any applet?

Bob



On Mon, Mar 14, 2011 at 10:39 PM, Otis Rothenberger  
wrote:

All-

Chemical Entities of Biological Interest (ChEBI) is dictionary of small 
molecular entities. While it understands SMILES, it does not have Jmol's 
ability to FIND SMILES. Nevertheless, one can query the dictionary with an 
InChiKey. With the help of NIH/NCI Resolver, therefore, a Jmol model can be 
used to directly query the dictionary:

http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='InChIKey=BSYNRY
MUTXBXSQ-UHFFFAOYSA-N'

with Resolver making the SMILES to InChiKey translation.

ChERBI is a user driven database that currently contains 18000 compounds. A 
brief discussion of ChEBI is here:

http://precedings.nature.com/documents/3525/version/1

>From a teaching perspective, this attracted my attention because it is a 
nice way to include bioinformatics into an instructional setting under the 
Jmol umbrella. While there are query accessible molfiles available via 
ChERBI, this is not the main point. Resolver and PubChem are much better 
general sources. The main point is that with one click in Jmol make the 
query, "Is the small molecule in my Jmol window of biological interest?" I 
have not yet hooked the CheMagic model kit to this site, but I expect to do 
so sometime this week.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org  


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phone: 507-786-3107

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


-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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


phone: 507-786-3107

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it is better to take what answer we get. 

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Re: [Jmol-users] Continuing Saga of Jmol Talking to Public Databases

Bob,

I think we still run into the cross domain security violation with the St 
Olaf server.

One possibility is to offer Jmol users simple server side scripts. ISU has 
certainly opened server side scripting for faculty. I suspect this may be 
true at other institutions. I only have experience with Windows servers. 
What would cover most bases if we went this route? Would Windows, Unix, and 
Mac get the job done?

I don't think I can handle the Mac and Unix side of this, but I'd certainly 
share my Resolver/PubChem ASP.NET script with anyone interested in this. If 
there are any Mac server of Unix server people who would like to give this 
a try, let me know, and I'll send you the script. The only condition is 
that you don't laugh at my chaotic scripting style.

Another Point: After our discussion a few weeks ago when you pointed out 
that Jmol script is completely synchronous, I've found that I no longer 
need AJAX. Jmol Script is AJAX! Actually, It's better. You don't need to 
keep saying, "Wait your turn." Every server touch waits patiently in a 
normal Jmol script line for its turn - no complaining no whining. It's 
great.

Some Continued Questions Related to Michael's Note:

1) Do you know if the applet running locally with a local file address is 
subject to disk writing restrictions?
2) Ignoring item 1 above entirely for a minute, what Michael suggests might 
be possible on a server. I'm effectively writing from Jmol to my server now 
by using server side scripting to write Jmol state. I should be able to 
write anything the Jmol puts into a string. That's half the battle. 
Michael, do you know if VB (more importantly for applications VBA) can 
read/write text to a Web server?

One Final Clarification:
When remote data comes into Jmol, I am no longer using AJAX - not for the 
query or the returned data. I am, of course, using the above ASP.NET 
script.
For a local database on my server, I am using AJAX. But this is only 
because I must first create a JSON structure and use it in JavaScript prior 
to Jmol coming into the picture.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Robert Hanson" 
Sent: Tuesday, March 15, 2011 7:30 AM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public 
Databases 

Speaking of public databases, this might be a time to test the facility 
that has been in Jmol for quite some time -- the ability of the UNSIGNED 
applet to access remote files via a JavaScript interface. I don't think 
anyone has capitalized on this, but there is a St. Olaf server that is 
built into Jmol.js. 


jmolLoadAjax_STOLAF_RCSB


Could we adapt this, Otis, to get small molecules into any applet?

Bob

On Mon, Mar 14, 2011 at 10:39 PM, Otis Rothenberger  
wrote:

All-

Chemical Entities of Biological Interest (ChEBI) is dictionary of small 
molecular entities. While it understands SMILES, it does not have Jmol's 
ability to FIND SMILES. Nevertheless, one can query the dictionary with an 
InChiKey. With the help of NIH/NCI Resolver, therefore, a Jmol model can be 
used to directly query the dictionary:

http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='InChIKey=BSYNRY
MUTXBXSQ-UHFFFAOYSA-N'

with Resolver making the SMILES to InChiKey translation.

ChERBI is a user driven database that currently contains 18000 compounds. A 
brief discussion of ChEBI is here:

http://precedings.nature.com/documents/3525/version/1

>From a teaching perspective, this attracted my attention because it is a 
nice way to include bioinformatics into an instructional setting under the 
Jmol umbrella. While there are query accessible molfiles available via 
ChERBI, this is not the main point. Resolver and PubChem are much better 
general sources. The main point is that with one click in Jmol make the 
query, "Is the small molecule in my Jmol window of biological interest?" I 
have not yet hooked the CheMagic model kit to this site, but I expect to do 
so sometime this week.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org  


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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

Re: [Jmol-users] I think the vibration animation state is being left out of the state...please check...

Oops, Jonathan is talking about "vibration on" not "animation on." I 
misunderstood the request. He definitely needs more checkers on this. I'm 
may have an appropriate SPARTAN file. If so, I'll check it.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Jonathan Gutow" 
Sent: Tuesday, March 15, 2011 9:24 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] I think the vibration animation state is being left 
out of the state...please check... 

Dear All:

I think the vibration animation state is being left out of the Jmol 
generated state script for versions of Jmol 12.0.26 and above (may have 
started earlier).   Can others please verify that when they save a state 
script for a molecule that is showing an animation of the vibration and 
reload the state script the reloaded molecule is not animated?

Thanks,
Jonathan
 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow


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Re: [Jmol-users] Continuing Saga of Jmol Talking to Public Databases

Michael,

OK, you definitely have my attention. Communication between Jmol and local 
applications is a great idea. I have a few questions:

1) Are you doing this with the applet or the application?

2) It sounds like you are currently "talking" to Jmol with your VB code 
independent of traditional applications - e.g. Excel, Word, etc. Is that 
correct?

3) Have you attempted to do this with an application, say Excel, using 
VBA?

>From Jmol's perspective, I think I understand why the file has to be 
written, but I don't see that as a big problem. I have a few other 
questions, but they are in the context of a reply to Bob's note. I think 
I'll post them in another email to this chain.

Otis

 

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Michael Marden" 
Sent: Tuesday, March 15, 2011 11:05 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public 
Databases 



  


  
  
Two items concerning communication with Jmol caught my attention.

this one (Continuing Saga of Jmol Talking to Public Databases)

and "Command line communication with the Jmolapplication?"


I'm not sure if it is really relevant to the method that I'm using.

I'm using visual basic (VB) as a front end, and Jmol shows up within
a browser (within a VB window).

So I can do all my set-up, calculations etc, and then send commands
to Jmol

Bob Hansen helped me set this up, using the Jmol.js and
JmolApplet.jar files.

The VB program writes a text file to disk that contains the
command.  Jmol is waiting and reads it back.


So essentially I continuously pump commands to modify the molecule
being presented.

I would prefer a way to avoid the round to the hard disk, but it
seems to work well.

As Jmol is now mature, it would be good to consider communication
with other programs.


Michael Marden

INSERM, University Paris 11, France 


On 15/03/2011 12:30, Robert Hanson wrote:
Speaking of public databases, this might be a time to
  test the facility that has been in Jmol for quite some time -- the
  ability of the UNSIGNED applet to access remote files via a
  JavaScript interface. I don't think anyone has capitalized on
  this, but there is a St. Olaf server that is built into Jmol.js. 


  

  jmolLoadAjax_STOLAF_RCSB

  


  Could we adapt this, Otis, to get small molecules into any applet?


  Bob


  On Mon, Mar 14, 2011 at 10:39 PM, Otis
Rothenberger 
wrote:

All-


Chemical Entities of Biological Interest (ChEBI) is
dictionary of small molecular entities. While it understands
SMILES, it does not have Jmol's ability to FIND SMILES.
Nevertheless, one can query the dictionary with an InChiKey.
With the help of NIH/NCI Resolver, therefore, a Jmol model
can be used to directly query the dictionary:



http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='InChIKey=BSYNRY
MUTXBXSQ-UHFFFAOYSA-N'


with Resolver making the SMILES to InChiKey translation.


ChERBI is a user driven database that currently contains
18000 compounds. A brief discussion of ChEBI is here:


http://precedings.nature.com/documents/3525/version/1


From a teaching perspective, this attracted my attention
because it is a nice way to include bioinformatics into an
instructional setting under the Jmol umbrella. While there
are query accessible molfiles available via ChERBI, this is
not the main point. Resolver and PubChem are much better
general sources. The main point is that with one click in
Jmol make the query, "Is the small molecule in my Jmol
window of biological interest?" I have not yet hooked the
CheMagic model kit to this site, but I expect to do so
    sometime this week.


Otis


  --
  

  Otis Rothenberger

  Department of Chemistry

  Illinois State University
  Normal, IL 61790-4160

  http://chemagic.org  
  


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Re: [Jmol-users] I think the vibration animation state is being left out of the state...please check...

Jonathan,

I'm using 12.1.35. With the cyclohexane chair flip, running the captured 
state seems to be starting the animation at the frame captured.

I don't think the state script will pass list size limits. I'll send it to 
you as an attachment for comparison to your state script. I tried to 
capture state close to the twisted boat. The first frame in the original 
file is a chair.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Jonathan Gutow" 
Sent: Tuesday, March 15, 2011 9:24 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] I think the vibration animation state is being left 
out of the state...please check... 

Dear All:

I think the vibration animation state is being left out of the Jmol 
generated state script for versions of Jmol 12.0.26 and above (may have 
started earlier).   Can others please verify that when they save a state 
script for a molecule that is showing an animation of the vibration and 
reload the state script the reloaded molecule is not animated?

Thanks,
Jonathan
 Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
 http://www.uwosh.edu/facstaff/gutow


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[Jmol-users] Continuing Saga of Jmol Talking to Public Databases

2011-03-14 Thread Otis Rothenberger

All-

Chemical Entities of Biological Interest (ChEBI) is dictionary of small 
molecular entities. While it understands SMILES, it does not have Jmol's 
ability to FIND SMILES. Nevertheless, one can query the dictionary with an 
InChiKey. With the help of NIH/NCI Resolver, therefore, a Jmol model can be 
used to directly query the dictionary:

http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='InChIKey=BSYNRY
MUTXBXSQ-UHFFFAOYSA-N'

with Resolver making the SMILES to InChiKey translation.

ChERBI is a user driven database that currently contains 18000 compounds. A 
brief discussion of ChEBI is here:

http://precedings.nature.com/documents/3525/version/1

>From a teaching perspective, this attracted my attention because it is a 
nice way to include bioinformatics into an instructional setting under the 
Jmol umbrella. While there are query accessible molfiles available via 
ChERBI, this is not the main point. Resolver and PubChem are much better 
general sources. The main point is that with one click in Jmol make the 
query, "Is the small molecule in my Jmol window of biological interest?" I 
have not yet hooked the CheMagic model kit to this site, but I expect to do 
so sometime this week.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
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[Jmol-users] moveto question

2011-03-05 Thread Otis Rothenberger

Bob,

In the following moveto from your cyclohexane flip, what does the negative 
time imply?

moveto -1.0 { -957 -245 155 101.12} 100.0 0.0 0.0 {0.75536114 1.1072346 
0.5814115} 3.7178335 {0.0 0.0 0.0} -8.276791 9.963518 0.0

Also, I just read your 2008 post on "what the heck is a quaternion," and 
I'm getting a clearer picture. I assume in the above cyclohexane moveto, 
you first set an initial rotation by hand and then captured it. Is that 
correct?

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
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Re: [Jmol-users] Really Ugly Windows Firefox Issue

2011-03-04 Thread Otis Rothenberger

Angel-
Thanks for the information. I'll try to update now. I don't think an update 
3.6.15 was expected. I think the next update was supposed to be 4.
Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Angel Herráez" 
Sent: Friday, March 04, 2011 3:14 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Really Ugly Windows Firefox Issue








I just got notice of the latest upgrade:




What's New in Firefox 3.6.15



Firefox 3.6.15 fixes the following issues found in previous versions of Firefox 
3.6:



* Fixed an issue where some Java applets would fail to load in Firefox 
3.6.14




It works now! Two page reloads, no problem in the applet.






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Re: [Jmol-users] Really Ugly Windows Firefox Issue

2011-03-03 Thread Otis Rothenberger

Angel-

It looks like they are aware of the problem:

https://support.mozilla.com/en-US/forums/contributors/705144

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org




 
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Re: [Jmol-users] Really Ugly Windows Firefox Issue

2011-03-03 Thread Otis Rothenberger

Angel-

Thanks for the feedback. I'm pretty sure it's a Firefox issue. I'm using an 
older version of Java (1.6.0_21), and your note indicates that you're seeing 
this with the latest Java update. Also, I noticed the problem immediately after 
the Firefox auto update.

I reload quite a bit during script development, and Firefox has another long 
standing issue - the endless count down (count up, actually) on reload. Unlike 
the current problem, this involves the applets second counting going on 
forever. The fix for this is also quitting Firefox. I never reported this 
because it takes a lot of reloads to see this, and I assumed I was pushing 
things with frequent reload. The current problem is much more severe, however.

I'm now going to report both issues.

Otis

--


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Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Angel Herráez" 
Sent: Thursday, March 03, 2011 4:23 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Really Ugly Windows Firefox Issue

Hi Otis

I was replying to say it's working for me, and about to hit 'Send',
but it is not!
First reload is Ok, but after 2 reloads as you said, the applet
freezes

   Win XP
   Firefox 3.6.14
   Oracle Java 1.6.0_24

Bad!

So is it Firefox or Java latest update that does this?

Chrome hasn't got the problem
IE8 is OK
Safari is OK
Opera is Ok


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[Jmol-users] Really Ugly Windows Firefox Issue

2011-03-02 Thread Otis Rothenberger

Applet0__6949575859348389__
defaults = "Jmol"
backgroundColor = "#33"
errorCallback = "errorCallback"
hoverCallback = "showmsg"
measureCallback = "measureCallback"
messageCallback = "showmsg"
pickCallback = "showpick"
scriptCallback = "scriptCallback"
language=en_US
defaultDirectory = "data"

FileManager.getAtomSetCollectionFromFile(caffeine.xyz)
FileManager opening 
http://chemapps.stolaf.edu/jmol/docs/examples-11/data/caffeine.xyz
The Resolver thinks Xyz
openFile(caffeine.xyz): 1983 ms
reading 24 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty 
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
24 atoms created
Time to autoBond: 17 ms
ModelSet: autobonding; use  autobond=false  to not generate bonds 
automatically
Jmol applet jmolApplet0__6949575859348389__ destroyed
Jmol applet jmolApplet0__345997870461704__ initializing
AppletRegistry.checkIn(jmolApplet0__345997870461704__)
applet context: -applet
appletDocumentBase=http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm


appletCodeBase=http://chemapps.stolaf.edu/jmol/docs/examples-11/
(C) 2009 Jmol Development
Jmol Version: 12.1.31  2011-01-17 00:12
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_21
os.name: Windows 7
memory: 3.0/16.3
processors available: 2
useCommandThread: false
appletId:jmolApplet0__345997870461704__
urlImage=jar:http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolApplet0.ja
r!/jmol75x29x8.gif
defaults = "Jmol"
backgroundColor = "#33"
errorCallback = "errorCallback"
hoverCallback = "showmsg"
measureCallback = "measureCallback"
messageCallback = "showmsg"
pickCallback = "showpick"
scriptCallback = "scriptCallback"
language=en_US
defaultDirectory = "data"

FileManager.getAtomSetCollectionFromFile(caffeine.xyz)
FileManager opening 
http://chemapps.stolaf.edu/jmol/docs/examples-11/data/caffeine.xyz
The Resolver thinks Xyz
openFile(caffeine.xyz): 143 ms
reading 24 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty 
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
24 atoms created
Time to autoBond: 1 ms
ModelSet: autobonding; use  autobond=false  to not generate bonds 
automatically
Jmol applet jmolApplet0__345997870461704__ destroyed
java.net.MalformedURLException: no protocol: JmolApplet0.jar
at java.net.URL.(Unknown Source)
at java.net.URL.(Unknown Source)
at sun.plugin.util.GrayBoxPainter.setProgressFilter(Unknown Source)
at sun.plugin2.applet.Plugin2Manager.setupGrayBoxPainter(Unknown 
Source)
at sun.plugin2.applet.Plugin2Manager.access$600(Unknown Source)
at 
sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown 
Source)
at java.lang.Thread.run(Unknown Source)
exception: name.
java.lang.IllegalArgumentException: name
at sun.plugin2.applet.Applet2ClassLoader.addJar(Unknown Source)
at sun.plugin2.applet.Applet2Manager.loadJarFiles(Unknown Source)
at 
sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown 
Source)
at java.lang.Thread.run(Unknown Source)
Exception: java.lang.IllegalArgumentException: name

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Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo

2011-02-28 Thread Otis Rothenberger

Incredible!

Load, frame all, and the following is instructive and fun to watch:

for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} 
ROTATE TRANSLATE 0.0;delay .5 }

Like I said. That file has been around for years, with lots of people 
asking about changing the C1 C2 fixed position. It's also nice to know the 
file's origin.

Otis

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Department of Chemistry

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Normal, IL 61790-4160

http://chemagic.org



From: "Robert Hanson" 
Sent: Monday, February 28, 2011 9:13 PM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo 


load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz
for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} 
ROTATE TRANSLATE 0.0 }

There are 35 models. This runs through the models, rotating and translating 
each model to be the best match to the previous model in the set. 
Originally written for aligning proteins, it turns out the COMPARE command 
does a pretty fair job with simple reactions as well.

Bob

On Mon, Feb 28, 2011 at 6:52 PM, Otis Rothenberger  
wrote:

Bob,

I can get the translated coordinates and frame adjustments from the state 
script of your page, so I have no problem loading your adjusted data for 
Hen's file. But I have looked at that file for years and said, "Boy I'd 
like to translate the those coordinates."

So, just as a Jmol learning exercise, how'd ya do it? I don't mean the 
details - just some gentle pointers.

Otis

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Department of Chemistry

Illinois State University
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http://chemagic.org



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Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo

2011-02-28 Thread Otis Rothenberger

Bob,

I can get the translated coordinates and frame adjustments from the state 
script of your page, so I have no problem loading your adjusted data for 
Hen's file. But I have looked at that file for years and said, "Boy I'd 
like to translate the those coordinates."

So, just as a Jmol learning exercise, how'd ya do it? I don't mean the 
details - just some gentle pointers.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org


 
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Re: [Jmol-users] Set Picking Eror

2011-02-24 Thread Otis Rothenberger

Thanks Angel. The top of your head works - so does "set picking none."

The document item at

http://chemapps.stolaf.edu/jmol/docs/index.htm?&fullmanual=1&ver=12.2#setpicking

should probably be edited. Actually, "set picking off" used to work, so maybe 
there is a bug.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Angel Herráez" 
Sent: Thursday, February 24, 2011 11:08 AM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Set Picking Eror

Otis,

from the top of my head, it used to be "set picking none"

But maybe the others are/were also valid


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[Jmol-users] Set Picking Eror

2011-02-24 Thread Otis Rothenberger

Bob,

With 12.1.35, I'm getting the following error with both set picking off and 
set picking false:

script ERROR: unrecognized SET PICKING SELECT parameter: false

 set picking >> false <<

I've not noticed this before because as it turns out most of my set picking 
off commands do not matter! I finally noticed it with a situation where 
picking off is required.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
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Re: [Jmol-users] Jmol version 12.x.xx and water molecule surface problem

2011-02-23 Thread Otis Rothenberger

Johannes-

I'm afraid I can't help, but I can confirm what your seeing:

1) Your file does not display MEP in 12.1.35.
2) A water molecule mol2 file that I created in Accelrys does not display 
MEP in 12.1.35
3) A water molecule Spartan file  not display MEP in 12.1.35
4) The following PubChem file DOES display MEP

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=962&disopt=3DDisplay
SDF

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Johannes Pernaa" 
Sent: Wednesday, February 23, 2011 11:06 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Jmol version 12.x.xx and water molecule surface 
problem 



  


  
  
Hi all.


I have a problem with water molecule electrostatic potential surface
in latest Jmol versions.


Example: 

When I try visualize them using Jmol 11.x.xx versions, everything
works fine, but 12.x.xx versions won't show it. 


All other molecules works just fine in 12.x.xx versions. Water
molecule is the only one that I can't get to work. I have tried
.spartan and mol.2 file types (see attachment).


Can anyone help me? 


Best regards

Johannes Pernaa


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Re: [Jmol-users] Bond picking woes

2011-02-17 Thread Otis Rothenberger

Angel and Adam,

To maintain model editing ability via script when NOT in modelkit mode is, I 
think, important. I find it essential. What may be useful here is a no action 
set picking assignBond_ ?? default that would just report bond picked.

Adam, I'm interested in your callback report. What I'm getting is not that 
verbose. I'm using set debugscript false. Are you using set debugscript true? 
Maybe that is more verbose. I have to check.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Angel Herráez" 
Sent: Thursday, February 17, 2011 2:15 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Bond picking woes

Oh, I didn't know this feature existed.

To me, changing bonds
1. is not suggested by the word "picking"
2. makes sense only in the context of ModelKit mode
3. could be implemented, if intended out of ModelKit mode, in the callback 
function, e.g.
using connect

Having bonds dissapear in normal Veiwer mode (which seems to make them 
unpickable, of
course) is rather worrying.

So I'd rather vote for a picking just reporting the atom IDs, not acting on the 
bond.

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Re: [Jmol-users] Bond picking woes

2011-02-17 Thread Otis Rothenberger

Angel and Adam,

I've been working under the assumption the set bondpicking true sets bond 
picking default behavior to changing bond order with the default order setting:

set picking assignBond_0

The call back information on this is of the following format (for ethane):

bond [{0}] "0"

Bug or not, I must admit that being able to intercept a bond click without 
action would be nice. One problem with the current callback in this regard is 
that you need the connection table - i.e. no connected  atom info in the 
callback.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Angel Herráez" 
Sent: Thursday, February 17, 2011 12:59 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Bond picking woes

Hello Adam

There is no reason why the bond should be deleted. This must be a
bug.
Please provide details of the exact version of Jmol you are using

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Re: [Jmol-users] SMILES Problem

2011-02-12 Thread Otis Rothenberger

Bob,

Some additional information to add some checks to this issue.

I pass the SMILES into Jmol Script from JavaScript, thus the // for / in 
the DB. I thought I better check the console entry of SMILES on an example 
that works. I was surprised by the results, but the NAD+ problem appears to 
be a problem with the SMILES. Here's the test example:

With prostacyclin I2 in the Jmol window, I tried all variations of the 
following, including changing "var z = {*}.find("SMILES",y);" to "var z = 
x.find("SMILES",y);" With both finds, I think I tried every combination of 
\\ and/or \. They all work! Do you have some type of auto correction for \ 
in the system?

var x = 
"C[C@H](O)/C=C/[C@@H]1[C@@H]2[C@H]3O/C/4=C\(O)=O.C\42.[C@H](O)1C3";


var y = 
"C[C@H](O)/C=C/[C@@H]1[C@@H]2[C@H]3O/C/4=C\(O)=O.C\42.[C@H](O)1C3";


var z = {*}.find("SMILES",y);
print @z

Anyway, the NAD+ problem remains. "var z = x.find("SMILES",y)" works, 
including apparent \\ vs \ irrelevancy. The var "z = {*}.find("SMILES",y)" 
with NAD+ in the window does not work.

Otis

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Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Otis Rothenberger" 
Sent: Saturday, February 12, 2011 3:54 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] SMILES Problem 

Bob,

For a model of NAD+, I have the following FIND problem.

SMILES strings are the same in both examples below.

THIS WORKS
var x = 
"NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=
O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[
n]%11.[n]%12=c%10.O54.O98";var cks = x.find('SMILES',x);print @cks

THIS DOES NOT WORK
var x = 
"NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=
O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[
n]%11.[n]%12=c%10.O54.O98";var cks = {*}.find('SMILES',x);print @cks

In the second case, "x" is pulled from a database via a query string query 
to the DB.

If I examine "x" directly from the DB created JSON structure via:

alert(oChem.models[0].smiJ)

I get

NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=O
.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[n
]%11.[n]%12=c%10.O54.O98

which looks OK.

If I examine {*).find("SMILES") directly from the console, I get:

NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=O
.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[n
]%11.[n]%12=c%10.O54.O98

which also looks OK.

The actual DB text is escaped as follows:

NC/1=O.C/2\\1=C/[N+1]/3=C/C=C\\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6
=O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=
[n]%11.[n]%12=c%10.O54.O98


This is the single case in a 1630 record database that does not work. Do 
you see anything in the above that might explain this? I'm stumped.

Otis

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http://chemagic.org 
 
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[Jmol-users] SMILES Problem

2011-02-12 Thread Otis Rothenberger

Bob,

For a model of NAD+, I have the following FIND problem.

SMILES strings are the same in both examples below.

THIS WORKS
var x = 
"NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=
O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[
n]%11.[n]%12=c%10.O54.O98";var cks = x.find('SMILES',x);print @cks

THIS DOES NOT WORK
var x = 
"NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=
O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[
n]%11.[n]%12=c%10.O54.O98";var cks = {*}.find('SMILES',x);print @cks

In the second case, "x" is pulled from a database via a query string query 
to the DB.

If I examine "x" directly from the DB created JSON structure via:

alert(oChem.models[0].smiJ)

I get

NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=O
.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[n
]%11.[n]%12=c%10.O54.O98

which looks OK.

If I examine {*).find("SMILES") directly from the console, I get:

NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=O
.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[n
]%11.[n]%12=c%10.O54.O98

which also looks OK.

The actual DB text is escaped as follows:

NC/1=O.C/2\\1=C/[N+1]/3=C/C=C\\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6
=O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=
[n]%11.[n]%12=c%10.O54.O98


This is the single case in a 1630 record database that does not work. Do 
you see anything in the above that might explain this? I'm stumped.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
--
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Pinpoint memory and threading errors before they happen.
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Re: [Jmol-users] extract min and max resNo to javascript

2011-01-25 Thread Otis Rothenberger

Son of a gun. The following works without any WAIT function:
var jmolSmiles = jmolEvaluate("{*}.find('SMILES')")
Unless it's in jmol.js and I don't see it?

Otis

--


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Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org


----
From: "Otis Rothenberger" 
Sent: Tuesday, January 25, 2011 7:39 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] extract min and max resNo to javascript 

Bob,
That's interesting. Does this mean that you do not have to use the WAIT?
Otis

  
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Re: [Jmol-users] extract min and max resNo to javascript

2011-01-25 Thread Otis Rothenberger

Bob,
That's interesting. Does this mean that you do not have to use the WAIT?
Otis

var x = eval(jmolEvaluate("[" + {*}.resno.min + "," + {*}.resno.max + "]"))

would get you both of them at once.

2011/1/25 Angel Herráez 

Hello all


This must be trivial, but I'm stuck


I need to extract the minimum and maximum residue nurmber from a one-chain pdb 
file into

a Javascript variable.

The Jmol commands are

  m1 = {*}.resno.min

  m2 = {*}.resno.max

but I don't know how to pass those to a javascript variable (I need to check 
user input against

them)


Thanks,

Angel


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Re: [Jmol-users] extract min and max resNo to javascript

2011-01-25 Thread Otis Rothenberger

Alex and Angel,
I think Alex's response is the "textbook" approach, but I've had real problems 
with jmolScriptWait. I don't think it's a bug. I just think it's susceptible to 
fussy waiting forever (hangs). As an alternative, I find that a call back works 
nicely. In the call back function below, the isolated line (marked **) is the 
key line. The variable etv1 is a Jmol global. The variable ETV1 is a JavaScript 
global. When I have a Jmol script value that I want to pass to JavaScript, I 
put it in evt1 and do a "print etv1." The isolated line (marked **) passes the 
callback value of etv1 to ETV1. In the function, the passing around of all the 
msg1 and msg2 values is a bit convoluted, but it's the only way I know to grab 
related msg1 and msg2 information! All the other lines in the function have to 
do with automating MINIMIZE during model editing or debug precessing. The key 
line at hand is only the isolated line and the msg1 msg2 shuffle.
Convolution aside, it works without hanging problems.
Otis

function processMessage(appNum, msg1, msg2) {msg1 = "" + msg1 + "";msg2 
= "" + msg2 + "";var num = 50;if (msg2.indexOf(") \"C\" {") < 0 || 
msg2.indexOf("assign connect") > -1) { num = 5; }if ((msg2.indexOf("assign 
connect") > -1 && ckModNum() > 1) || msg2.indexOf("}] \"0\"") > -1) { num = 50; 
}

**if (msg2Old.indexOf("print etv1") > -1) { ETV1 = msg1; }

if (msg2Old.indexOf("print {*}.find('SMILES')") > -1) { jmolSmiles = msg1; 
}if (msg2.indexOf("assign atom") > -1 || msg2.indexOf("assign connect") > 
-1 || msg2.indexOf("assign bond") > -1) { doUFF(num); }if (jmolDebugOn) { 
memVar1 += msg1 + "~"; memVar2 += msg2 + "~"; }msg1Old = msg1;msg2Old = 
msg2;}

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Alexander Rose" 
Sent: Tuesday, January 25, 2011 7:07 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] extract min and max resNo to javascript

Hi,

I think you can build on this:

jmolScriptWait('var foo = "bar";');
var msg = jmolEvaluate( "script('echo @foo');" );

Alex

Am 26.01.2011 um 01:05 schrieb Angel Herráez:

> Hello all
>
> This must be trivial, but I'm stuck
>
> I need to extract the minimum and maximum residue nurmber from a one-chain 
> pdb file into
> a Javascript variable.
> The Jmol commands are
>  m1 = {*}.resno.min
>  m2 = {*}.resno.max
> but I don't know how to pass those to a javascript variable (I need to check 
> user input against
> them)
>
> Thanks,
> Angel
>
>
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[Jmol-users] PubChem Again

2011-01-22 Thread Otis Rothenberger

This is not perfect, but it's pretty good. It's a follow up to Bob's 
PubChem SDF partial charge reader:

If you go to our model kit application:

http://chemagic.com/web_molecules/script_page_large.aspx

and put a model in the Jmol window (JME draw it, modelkit constructed it, 
whatever...), then you can load the PubChem SDF for this model by the 
following sequence:

1) Go to the Tools menu and click the PubChem link. Two new links will 
appear

Open Search Results Page AND Get PubChem SDF File

2) Click the Get PubChem SDF File link. If the SDF data is found, a new 
link appears

Load PubChem SDF File

Click this link to load the PubChem SDF. The value of this is that many 
PubChem SDF's have partial charge data. On the above Tools menu, the MEP 
links should verify this.

The convolution of two clicks to get this job done is required by the fact 
that the direct load of an SDF from PubChem requires a PubChem CID. Since 
the NIH/NCI Resolver does not yet resolve PubChem CID's, I have to make 
PubChem do this for me. This is done by passing the Resolver accessible 
InchiKey of a Jmol model (via SMILES) to PubChem. Subsequently, an entire 
Web page has to be parsed, and this is a mess! For anyone interested in 
trying this, I offer the following "Resolver" on the ISU Chemistry 
Department server:

http://chemistry.illinoisstate.edu/osrothen/web_molecules/nih.aspx?cid=LFQSC
WFLJHTTHZ-UHFFFAOYSA-N

The query string is simply the InchiKey for the model. The return is either 
the PubChem CID text string or the string "Translation" if there is an 
error.

I have rigged this "Resolver" so that an SDF false (the string 
"Translation" ) comes back if there is NOT a unique PubChem hit. PubChem 
will return a list of possible related structures if it can't exactly match 
an InchiKey. Since the correct SDF may or may not be in this list, I return 
the false.

If you have not played with the Real Resolver's InchiKey for SMILES 
translation, then here is the URL for ethanol:

http://cactus.nci.nih.gov/chemical/structure?string=CCO&representation=stdin
chikey

Otis

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Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
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Re: [Jmol-users] PubChem SDF

2011-01-19 Thread Otis Rothenberger

Bob,

Hmmm...  That's what I was thinking you might do also. It all works fine - 
thanks.

I sent a note to Markus re PubChem CIDs. If Resolver could include these, 
that would sure make the next step easier.

Just a thought: One of the first things in learning a new programming 
language is the old Hello World routine. The initial inclusion of SMILES in 
Jmol and more specifically your subsequent work with this initial inclusion 
has allowed Jmol to shout Hello World quite loudly,  AND Jmol is getting 
some pretty good answers. In addition to the model kit stuff, I'm having a 
pretty good time playing with this two way communication ability, and I 
think we're just scratching the surface of what's possible.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Robert Hanson" 
Sent: Wednesday, January 19, 2011 1:26 AM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] PubChem SDF 

yup, that's what I was thinking you might do. OK, I will implement that. 

see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

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. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

 
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Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Otis Rothenberger

Bob,

I'm not sure how stable it is, but the JS function below works. I'm also 
not sure how cross browser (platform) friendly it is. My Mac buddy is OOO 
for six weeks.

If a PubChem molfile with partial chages is pasted into our model kit 
script field on the Molecular Editor screen and then run, the PubChem model 
will load with partial charges:

http://chemagic.com/web_molecules/script_page_large.aspx

In the function, I display the MEP on load because that seems to light-up 
the Jmol menu's Surfaces/MEP selection, but this light-up is erratic. 
Nevertheless, Jmols script will display the MEP. Here are three PubChem SDF 
links for getting cut/paste files for testing:

cholesterol
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5997&disopt=3DDispla
ySDF

benzoquinone
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=4650&disopt=3DDispla
ySDF

And a pretty one Aspirin
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2244&disopt=3DDispla
ySDF

In some cases the charges are pretty primitive, but the MEP's get the point 
across. As you can see above, direct loading of the file requires the 
PubChem CID. By finagling, I think these can be pulled from a PubChem 
InChiKey query via Resolver. More to the point, I'm going to write to 
Markus about the possibility of Resolver returning PubChem CID's directly 
on a SMILES query. I'm betting these are already in Resolver's many 
database connections.

Even if this does not work out, the PubChem SDF's are available via a name 
search and two clicks at the PubChem site. This puts MEP display for lots 
of models within reach of high school chemistry classes. What I'm really 
after, however is:

1) Draw a simple structure in JME
2) Load it into Jmol
3) Click a link that takes you to PubChem for this Model
We have it to this point. The last is within reach.
4) Load the MEP of the model that started in JME directly from PubChem 
data.

The JS function, in my usual verbose and chaotic style, follows.

Otis

function pcpc() {
var mf = document.getElementById("script").value;
if (mf.toUpperCase().indexOf("PUBCHEM_MMFF94_PARTIAL_CHARGES") < 0) { 
return; }
mf = mf.replace(/(\r\n|\n|\r)/gm, "|");
var scpt1 = ""; var scpt2 = "";
var re = /PARTIAL_CHARGES>\|(.*?)\|\|/;
var chgis;
var chgDs = mf.match(re);
var chgs = chgDs[1].split("|");
for (var x = 1; x <= chgs[0]; x++) {
chgis = chgs[x].split(" ");
scpt1 += "{atomno=" + chgis[0] + "}.partialCharge=" + chgis[1] + 
";"
}
scpt2 = "{*}.partialCharge = 0;" + scpt1 + "isosurface vdw 80% map mep 
translucent;";
jmolScript(scpt2);
}

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Robert Hanson" 
Sent: Tuesday, January 18, 2011 6:55 PM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] PubChem SDF 

Of course, Otis is so good at JavaScript, he could easily write a little 
JavaScript parser for this;)

 
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Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Otis Rothenberger

Thanks for the reply Angel.

I
 suspect PubChem is pretty much married to this system. Between
JavaScript and Jmol script, I think I can import and the partial charge
information.

The PubChem SDF's are "GET-able" with a PubChem CID,
 so these files will import directly into Jmol. Jmol reads the
coordinates OK. I'll just grab the charge data and add it via scripting.

The
 catch in this whole plan is the PubChem CID. You need it before you can
 do a direct GET. Fortunately, there's a whole blog cottage industry
that deals with accessing PubChem data directly, so I think I can set
this all up. I have three potential plans at this point, including a
PubChem API that turns a POST into an appropriate GET query.

In
answer to your question on other software, the only thing I've seen is
academic chemometric discussion lists that discuss converting the
PubChem data to mol2 for their own systems.

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Angel Herráez" 
Sent: Tuesday, January 18, 2011 5:18 AM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] PubChem SDF

Just my 2 cents:

> Evidently, a fair number of PubChem's sdf's have partial charge data.

I see aproblem here. The format shown in your example is not
according to SDF spec (I think it does not suppor partial charge,
only formal charge). They shouldbe using a different format, like
MOL2.

So if Jmol is made to support reading that, it is not really SDF
import. That should be made clear.

What other software reads those PubChem SDF files?


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[Jmol-users] PubChem SDF

2011-01-17 Thread Otis Rothenberger

Bob,

Evidently, a fair number of PubChem's sdf's have partial charge data. I 
know that I can parse the data with JavaScript and apply the charge 
results, including implied zeros, to the model with Jmol script, but I want 
to make sure I'm not reinventing the wheel. I've pasted the data for 
ethanol below. Is Jmol able to read these partial charges directly?

Otis

702
  -OEChem-01171122093D

  9  8  0 0  0  0  0  0  0999 V2000
   -1.17120.29970. O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0463   -0.56650. C   0  0  0  0  0  0  0  0  0  0  0  0
1.21750.26680. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0958   -1.21200.8819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0952   -1.1938   -0.8946 H   0  0  0  0  0  0  0  0  0  0  0  0
2.1050   -0.3720   -0.0177 H   0  0  0  0  0  0  0  0  0  0  0  0
1.24260.9307   -0.8704 H   0  0  0  0  0  0  0  0  0  0  0  0
1.26160.90520.8886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.12910.83640.8099 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  9  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
M  END
> 
702

> 
0.4

> 
1

> 
3
1 -0.68
2 0.28
9 0.4

> 
0

> 
2
1 1 acceptor
1 1 donor

> 
3

> 
0

> 
0

> 
0

> 
0

> 
0

> 
1

> 
1

> 
02BE0001

> 
-1.3096

> 
10.148

> 
139733 1 18410856559692628036
21015797 1 18196933258125981446

> 
55.87
1.48
0.75
0.58
0.11
-0.18
0
0
0.06
0.15
0
0
0.09
-0.67

> 
84.621

> 
41.5

> 
2
5
255



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Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
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Re: [Jmol-users] Edited Model Question

2011-01-12 Thread Otis Rothenberger

Bob,


Got it. Thanks.


Now that you point me, I also see a "atomName set." These strings will let 
me set the JavaScript globals.


Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Robert Hanson" 
Sent: Wednesday, January 12, 2011 1:33 PM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Edited Model Question 

you will see a bunch of connect commands and probably load data 

On Wed, Jan 12, 2011 at 10:58 AM, Otis Rothenberger  
wrote:

Bob,

Is there any unique marker in the model state text that would identify a 
model as having been edited?

My interest in this is to pick up this information when a remote user loads 
a model state saved by another user. In our application, I have JavaScript 
that treats an edited model differently than an unedited model. Locally, I 
can hold the editing status in a global variable. This global, of course, 
will not be set properly on the remote users computer. I can pass this 
information with the state text and parse it on the other end, but if the 
information is already in the state text, I'll set the remote global with 
that.

The new state transfers between multi users seem faster. My imagination or 
has something changed to make state reading and loading faster?

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org  


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[Jmol-users] Edited Model Question

2011-01-12 Thread Otis Rothenberger

Bob,

Is there any unique marker in the model state text that would identify a 
model as having been edited?

My interest in this is to pick up this information when a remote user loads 
a model state saved by another user. In our application, I have JavaScript 
that treats an edited model differently than an unedited model. Locally, I 
can hold the editing status in a global variable. This global, of course, 
will not be set properly on the remote users computer. I can pass this 
information with the state text and parse it on the other end, but if the 
information is already in the state text, I'll set the remote global with 
that.

The new state transfers between multi users seem faster. My imagination or 
has something changed to make state reading and loading faster?

Otis

--


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Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org 
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Re: [Jmol-users] Extract Molfile

2011-01-10 Thread Otis Rothenberger

Bob,

It looks like the problem is V2000 standards. V3000 has an actual CHG 
block. In V2000 atom block reference to charge, the following is used:

0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1,
4 = doublet radical, 5 = -1, 6 = -2, 7 = -3

Bizarre! Symyx reference:

http://www.symyx.com/downloads/public/ctfile/ctfile.jsp

Otis 

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: "Otis Rothenberger" 
Sent: Monday, January 10, 2011 2:17 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Extract Molfile 

Bob,

I see that version 12.1.30_dev produces a more structured molfile on 
Extract that includes charge data. That's neat.

This did break one of my scripts, and I can't find the problem. The broken 
script involves a single model duplication. In this script, first the data 
is extracted:

var modTxt = 'echo Copying model data...;mod1 = "' + 
jmolGetPropertyAsString("extractModel", "all") + '";javascript 
"dupMod2()";';
jmolScript(modTxt);

dupMod2() then does the following:

var scpt = 'delay 1;echo;var i = {*}.atomIndex.max + 1;var t = 
{*}.atomIndex.min;select within(branch, {atomIndex = i}, {atomIndex=t});var 
x = {selected}.size;var y={*}.size;var z = y - x;';
scpt += 'if (y > 40 || z != 0){echo This feature is limited to a single 
model with|less than 40 atoms.;delay 3;echo;}';
scpt += 'else{var sz = 5;if (y > 8){sz = 6};if (y > 11){sz = 7};if (y > 
30){sz = 9};set appendNew false;';
scpt += 'select *;translateSelected {...@sz @sz 0};load APPEND "@mod1";';
scpt += 'mod1="";hover off;' + loadScpt + 'select *;wireframe 
0.15;spacefill 23%;boundbox {*};centerat boundbox;javascript 
"getFormula();lnkSwitch()";}';
jmolScript(scpt);

The global variable loadScpt is just some echo and label settings. For 
neutral models the above still works, but if I have an original  ion, I end 
up with charge problem. By way of example duplicating the 2-propyl cation 
results in the following (end of email) extracted molfile for the two 
models. Note the duplicated cation is now +3.

I've run into conflicting standards for charges in the molfile atom block 
before. Some standards use actual charges while others use an integer 
code!!! Is that what's going on here, or do you see a problem with my 
code??

Otis

string
__Jmol-12_01101114153D 1   1.0 0.0 0
Jmol version 12.1.30_dev  2010-12-06 22:36 EXTRACT: ({0:5 8:21})
 20 18  0  0  0  0  1 V2000
  -5.25897   2.94760  -5.22727 C   0  0  0  0  0  0
  -6.40696   3.88045  -4.97901 C   0  1  0  0  0  0
  -5.19679   2.67627  -6.29968 H   0  0  0  0  0  0
  -5.40453   2.03269  -4.62526 H   0  0  0  0  0  0
  -4.32125   3.44406  -4.91922 H   0  0  0  0  0  0
  -6.57636   4.30536  -3.56545 C   0  0  0  0  0  0
  -5.64464   4.81988  -3.22194 H   0  0  0  0  0  0
  -6.73390   3.40107  -2.92615 H   0  0  0  0  0  0
  -7.43260   4.98898  -3.43879 H   0  0  0  0  0  0
  -7.07100   4.22428  -5.77467 H   0  0  0  0  0  0
  -0.31570   0.36779   0.60032 C   0  0  0  0  0  0
   0.29552  -0.34440  -0.56970 C   0  3  0  0  0  0
   0.12635   0.01278   1.55223 H   0  0  0  0  0  0
  -1.40380   0.17640   0.60730 H   0  0  0  0  0  0
  -0.13472   1.45247   0.49351 H   0  0  0  0  0  0
  -0.23199   0.06232  -1.89775 C   0  0  0  0  0  0
  -0.05836   1.15762  -2.04269 H   0  0  0  0  0  0
  -1.33430  -0.12533  -1.92861 H   0  0  0  0  0  0
   0.25017  -0.49061  -2.72136 H   0  0  0  0  0  0
   1.07055  -1.10543  -0.45844 H   0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  1  4  1  0  0  0
  1  5  1  0  0  0
  2  6  1  0  0  0
  7  6  1  0  0  0
  8  6  1  0  0  0
  9  6  1  0  0  0
 10  2  1  0  0  0
 11 12  1  0  0  0
 11 13  1  0  0  0
 11 14  1  0  0  0
 11 15  1  0  0  0
 12 16  1  0  0  0
 17 16  1  0  0  0
 18 16  1  0  0  0
 19 16  1  0  0  0
 20 12  1  0  0  0
M  END

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http://chemagic.org 
 
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[Jmol-users] Extract Molfile

2011-01-10 Thread Otis Rothenberger

Bob,

I see that version 12.1.30_dev produces a more structured molfile on 
Extract that includes charge data. That's neat.

This did break one of my scripts, and I can't find the problem. The broken 
script involves a single model duplication. In this script, first the data 
is extracted:

var modTxt = 'echo Copying model data...;mod1 = "' + 
jmolGetPropertyAsString("extractModel", "all") + '";javascript 
"dupMod2()";';
jmolScript(modTxt);

dupMod2() then does the following:

var scpt = 'delay 1;echo;var i = {*}.atomIndex.max + 1;var t = 
{*}.atomIndex.min;select within(branch, {atomIndex = i}, {atomIndex=t});var 
x = {selected}.size;var y={*}.size;var z = y - x;';
scpt += 'if (y > 40 || z != 0){echo This feature is limited to a single 
model with|less than 40 atoms.;delay 3;echo;}';
scpt += 'else{var sz = 5;if (y > 8){sz = 6};if (y > 11){sz = 7};if (y > 
30){sz = 9};set appendNew false;';
scpt += 'select *;translateSelected {...@sz @sz 0};load APPEND "@mod1";';
scpt += 'mod1="";hover off;' + loadScpt + 'select *;wireframe 
0.15;spacefill 23%;boundbox {*};centerat boundbox;javascript 
"getFormula();lnkSwitch()";}';
jmolScript(scpt);

The global variable loadScpt is just some echo and label settings. For 
neutral models the above still works, but if I have an original  ion, I end 
up with charge problem. By way of example duplicating the 2-propyl cation 
results in the following (end of email) extracted molfile for the two 
models. Note the duplicated cation is now +3.

I've run into conflicting standards for charges in the molfile atom block 
before. Some standards use actual charges while others use an integer 
code!!! Is that what's going on here, or do you see a problem with my 
code??

Otis

string
__Jmol-12_01101114153D 1   1.0 0.0 0
Jmol version 12.1.30_dev  2010-12-06 22:36 EXTRACT: ({0:5 8:21})
 20 18  0  0  0  0  1 V2000
  -5.25897   2.94760  -5.22727 C   0  0  0  0  0  0
  -6.40696   3.88045  -4.97901 C   0  1  0  0  0  0
  -5.19679   2.67627  -6.29968 H   0  0  0  0  0  0
  -5.40453   2.03269  -4.62526 H   0  0  0  0  0  0
  -4.32125   3.44406  -4.91922 H   0  0  0  0  0  0
  -6.57636   4.30536  -3.56545 C   0  0  0  0  0  0
  -5.64464   4.81988  -3.22194 H   0  0  0  0  0  0
  -6.73390   3.40107  -2.92615 H   0  0  0  0  0  0
  -7.43260   4.98898  -3.43879 H   0  0  0  0  0  0
  -7.07100   4.22428  -5.77467 H   0  0  0  0  0  0
  -0.31570   0.36779   0.60032 C   0  0  0  0  0  0
   0.29552  -0.34440  -0.56970 C   0  3  0  0  0  0
   0.12635   0.01278   1.55223 H   0  0  0  0  0  0
  -1.40380   0.17640   0.60730 H   0  0  0  0  0  0
  -0.13472   1.45247   0.49351 H   0  0  0  0  0  0
  -0.23199   0.06232  -1.89775 C   0  0  0  0  0  0
  -0.05836   1.15762  -2.04269 H   0  0  0  0  0  0
  -1.33430  -0.12533  -1.92861 H   0  0  0  0  0  0
   0.25017  -0.49061  -2.72136 H   0  0  0  0  0  0
   1.07055  -1.10543  -0.45844 H   0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  1  4  1  0  0  0
  1  5  1  0  0  0
  2  6  1  0  0  0
  7  6  1  0  0  0
  8  6  1  0  0  0
  9  6  1  0  0  0
 10  2  1  0  0  0
 11 12  1  0  0  0
 11 13  1  0  0  0
 11 14  1  0  0  0
 11 15  1  0  0  0
 12 16  1  0  0  0
 17 16  1  0  0  0
 18 16  1  0  0  0
 19 16  1  0  0  0
 20 12  1  0  0  0
M  END

--


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http://chemagic.org 
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Re: [Jmol-users] MEP Surface Problem

2011-01-09 Thread Otis Rothenberger

Bob,

If it helps, this is my message call back on MEP and VDW from the Jmol 
menu:

isosurface1 created with cutoff=NaN min=0.0 max=0.0; number of isosurfaces 
= 0

The following point is not a problem, but I'll mention it because it might 
be related:

isosurfaceArea

The used to back as a decimal for a non-split surface. It now comes back as 
an array with one item.

Otis

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From: "Otis Rothenberger" 
Sent: Sunday, January 09, 2011 10:59 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] MEP Surface Problem 

Bob,

Molecular Electrostatic Potential appears to be broken on 12.1.30_dev. I 
can't map the surface via the Jmol menu or Jmol script on my page. The Jmol 
menu sees that partial charges are there, but no mapping occurs.

Otis

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[Jmol-users] MEP Surface Problem

2011-01-09 Thread Otis Rothenberger

Bob,

Molecular Electrostatic Potential appears to be broken on 12.1.30_dev. I 
can't map the surface via the Jmol menu or Jmol script on my page. The Jmol 
menu sees that partial charges are there, but no mapping occurs.

Otis

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Re: [Jmol-users] Partial Wrap Up of the Coordination Issue

2011-01-03 Thread Otis Rothenberger

Bob,

OK, thanks.

That fixed the problem. I've generalized our use of minimize FIX so it 
works with any central atom in place, thus locking the geometry of this 
atom and attached atoms during subsequent editing. Using this system, Tom 
can draw carboplatin in Jmol in seconds without loss of Pt geometry during 
the editing, providing he starts with a custom square planar template. He's 
working on isomer/stereochemistry exercises, and the compare function seems 
to be working well. I had put this coordination stuff on a back burner, so 
I'm glad he got me started again.

Otis

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http://chemagic.org



From: "Robert Hanson" 
Sent: Monday, January 03, 2011 11:31 AM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: Partial Wrap Up of the Coordination Issue 

It was a bug with the H atom addition. See fixed: 
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

 
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[Jmol-users] Coordination Models Again

2011-01-02 Thread Otis Rothenberger

Bob,

We're making some progress with the construction of coordination models. 
The challenge is to find an approach that makes central atom geometry hold 
up under UFF and Resolver minimization, but allow for minimization on other 
parts of the evolving model. I have linear, trigonal planar, square planar, 
octahedral, and of course tetrahedral under control. Trigonal bipyramidal 
is a problem. It seems that minimize FIX should be ideal for this, but it's 
not working for me. Here's the script:

select phosphorus OR connected(phosphorus);minimize FIX {selected}

Am I correct in the assumption that the above should hold P and any atom 
directly connected to P fixed during minimize? I get confused about the 
logical and/or in these statements, but neither seems to work. Although 
it's counter intuitive to me, I think OR is correct. Again AND and OR 
fail.

Otis

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[Jmol-users] Extract Molfile

2010-12-30 Thread Otis Rothenberger

Bob,

This probably should go on the feature request page, but I'll post a 
feasibility question here. How hard would it be to set Extract molfile to 
include stereo bond information? Alternatively, could Jmol write JME 
files?

My intention here is to retain stereo information when a Jmol model is read 
into JME editor (depicted). Either approach (JME file or stereo bond 
encoded molfile) will work.

I have agendas associated with this too numerous to mention here!

Otie

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[Jmol-users] Another Useful External Connection for Jmol

2010-12-27 Thread Otis Rothenberger

I found a useful HNMR Jmol connection to complement the NIST Webbook IR/MS 
connection that I mentioned in a previous post. This HNMR connection is at 
the following site:

http://www.nmrdb.org/

The page author is Dr. Luc Patiny:

http://cheminformatics.epfl.ch/

The HNMR page has an NMR prediction engine that takes a SMILES query. The 
SMILES query format is shown below:

http://www.nmrdb.org/predictor?smiles=C

The NMR prediction engine will not accept SMILES dot notation, but once 
again the NIH/NCI Chemical Resolver can solve this communication problem. 
The information flow is:

Jmol model ---> Jmol SMILES ---> Resolver SMILES ---> 
http://www.nmrdb.org/predictor?smiles=XXX

Once again, a working example is at 
http://chemagic.com/web_molecules/script_page_large.aspx  The Model Tools 
link, followed by Predict HNMR

Otis

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Re: [Jmol-users] Another Resolver Thought

2010-12-18 Thread Otis Rothenberger

Bob,

One last thought on this chain.

As you can see, I've developed a bit of interest in connecting Jmol to 
outside data other than sdf data using Resolver to translate as needed. 
I've focused on three databases for a variety of reasons:

1) NIST WebBook IR/MS data - Uses InChI query - Limited db, but good for 
advanced model kit problems.

2) PubChem - Uses InChI query - Huge db, and excellent for model kit 
"see what you created" exercises.

3) CAS Common Chemisty Service - Uses CAS# query - Limited db, but with 
a focus on public outreach (a magic word for me).

All of the above are easy to link to the model in the Jmol window using 
the methods in this chain. The latter is particularly nice for high 
school level. Under an ongoing cooperative effort with Wikipedia, the 
CAS# search return gives a direct link to the Wikipedia article that 
matches the CAS# if an article exists. One problem with CAS# query is 
the proliferation of CAS#'s. Resolver returns them all. Only one is 
reliable, and its location in the Resolver return appears random. A 
filter of the returned data for the shortest CAS# seems to work. It's 
also a good idea to strip SMILES stereochemistry (@) before the Resolver 
SMILES to CAS# translation.

I'd like an item (4) above - nmr data. I can't find a source suited to 
our methodology, however.  SDBS Compounds and Spectral Search would be 
nice, but there is no query access. I'll write to them, but I don't have 
high hopes. They use a disclaimer screen that seems to be important to 
their data release approach. Perhaps they would be agreeable to Jmol 
users arriving at the disclaimer with a CAS# good to go.

As usual, an operational example is at

http://chemagic.com/web_molecules/script_page_large.aspx

Use Tools menu.

Otis

Otis Rothenberger
chemagic.com

On 12/14/2010 11:37 AM, Robert Hanson wrote:
> I see, so what you mean you are interested in doing is to display the 
> WebBook page for a given structure in Jmol. Yes, that would need some 
> JavaScript. Just change your "stdinchikey" to "stdinchi" in that first 
> call and you will get the InChiI, not the key. Then you don't strip 
> anything; just trim the line and insert it, since it already starts 
> with "InChI="
>
> Interesting!
>
> Bobinfo/jmol-users

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Re: [Jmol-users] Another Resolver Thought

2010-12-13 Thread Otis Rothenberger

Bob,

 From the console, either seems to work. But to finish this thought for 
folks who might want to try it (i.e. hooking the InChI for a loaded Jmol 
model to external database like NIST) with the signed applet, the 
returned InChI must go into a JavaScript variable needed to write the 
data link. You explained this process to me a while back, so I'll post 
the process here for completeness:

If from the location window, you enter:

javascript: jmolScript("nihstuff = 
load('http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchikey').trim()")

Then the following would illustrate how to get Jmol nihstuff into a 
JavaScript variable:

javascript: var jmTojs = jmolEvaluate("@nihstuff"); alert(jmTojs )

The alert: InChIKey=IJDNQMDRQITEOD-UHFFFAOYSA-N

As I mentioned earlier, I thought that I was using InChI - not InChIKey. 
It does not matter. Ether way, the URL has the following structure:

http://webbook.nist.gov/cgi/cbook.cgi?InChI=IJDNQMDRQITEOD-UHFFFAOYSA-N&Units=SI

I just strip out the InChIKey=, and construct the following:

var urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI="; + jmTojs + 
"&Units=SI&cIR=on&cMS=on"

Finally, an open.window() will produce pop-up headaches. Consequently, I 
write a dynamic link to make the user take the pop-up legal action.

Otis

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Re: [Jmol-users] Another Resolver Thought

2010-12-13 Thread Otis Rothenberger


Bob,

I'm just after data (spectra, iupac names, etc). I never thought about 
loading the sdf files. I'll look into that. But...


Will file() load data from a remote URL? Here's the appropriate info:

http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchikey

Recall that Markus added this standard approach to the Resolver query 
string, so the above will return the InChI for butane. Actually, it's 
returning the InChIKey. I thought I changed that to InChI, but whatever. 
Can the signed applet read this directly? The idea here is to use this 
InChI to load the NIST spectral data for the model in the window by 
creating a dynamic link via JavaScript:


urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI="; + nihInchi + 
"&Units=SI&cIR=on&cMS=on"


urlNm becomes the href for the dynamic link, and the user can thus load 
NIST spectral data directly for the model in the window.


Otis


Otis Rothenberger
chemagic.com


On 12/13/2010 4:03 PM, Robert Hanson wrote:
If you have the signed applet, there should be no need for server-side 
scripting. Just use the


file()

function to load the contents of the resolver file -- which would be 
the InChI string, right? Then send the proper load command to Jmol.


Bob

On Mon, Dec 13, 2010 at 2:46 PM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


All,

While working on a structure database for our Jmol application, I
found
myself spending a lot of time searching PubChem and the NIST
Webbook. In
all cases, I was searching a model that was already in the Jmol
window.
This falls into the category of the obvious finally hitting me:
Jmol can
hook directly to PubChem and NIST Webbook via query string request
passed through NCI/NIH Resolver. I was doing this manually because
neither of these databases uses a SMILES query string. With Resolver,
however, the following is possible:

Jmol SMILES >  Resolver InChI > NIST or PubChem Query

The appropriate URL structure is below. I have NIST set for IR/MS:

urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI="; + nihInchi +
"&Units=SI&cIR=on&cMS=on"

urlNm =
"http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=
<http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=>" +
nihInchi + "+i"

This would require the signed applet and access to server side
scripting. If a Resolver InChI query is added to Jmol, the signed
applet
should work without server side scripting.

The double hit schematic above (Resolver then NIST/PubChem) leads to
pop-up blocker problems. I get around this by writing a dynamic "Click
for Search Results" link using the information returned from Resolver.
An example can be found at:

http://chemagic.com/web_molecules/script_page_large.aspx

Follow "The Model Tools" link.

Otis



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[Jmol-users] Another Resolver Thought

2010-12-13 Thread Otis Rothenberger

All,

While working on a structure database for our Jmol application, I found 
myself spending a lot of time searching PubChem and the NIST Webbook. In 
all cases, I was searching a model that was already in the Jmol window. 
This falls into the category of the obvious finally hitting me: Jmol can 
hook directly to PubChem and NIST Webbook via query string request 
passed through NCI/NIH Resolver. I was doing this manually because 
neither of these databases uses a SMILES query string. With Resolver, 
however, the following is possible:

Jmol SMILES >  Resolver InChI > NIST or PubChem Query

The appropriate URL structure is below. I have NIST set for IR/MS:

urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI="; + nihInchi + 
"&Units=SI&cIR=on&cMS=on"

urlNm = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term="; + 
nihInchi + "+i"

This would require the signed applet and access to server side 
scripting. If a Resolver InChI query is added to Jmol, the signed applet 
should work without server side scripting.

The double hit schematic above (Resolver then NIST/PubChem) leads to 
pop-up blocker problems. I get around this by writing a dynamic "Click 
for Search Results" link using the information returned from Resolver. 
An example can be found at:

http://chemagic.com/web_molecules/script_page_large.aspx

Follow "The Model Tools" link.

Otis



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[Jmol-users] Jmol SMILES

2010-12-08 Thread Otis Rothenberger

Bob,

I was working on some model exercises involving addition to Re and Si 
carbonyl faces.  Using the model kit to form the alcohol from 
para-chlorobenzophenone, the resulting (4-chlorophenyl)-phenylmethanol 
SMILES shows no R/S stereochemisty. Subsequent playing around with other 
substituted diphenylcarbinols, including ring alkyl substituents, showed 
the same type of result.

Bug or inherent kekule aromatic SMILES limitation?

Otis

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Re: [Jmol-users] Random Bond Picking Event

2010-12-06 Thread Otis Rothenberger


Bob,

Well, the third dimension enters into this. This is one of those events 
that hits randomly, and you have to work to set it up to analyze it.


If you take 2-butanone and line it up so the carbonyl is vertical, the 
event becomes likely. When the event hits under these conditions, 
tilting the model forward or backward slightly so that the carbonyl 
stays in the YZ plane does not fix the problem. If you break out of the 
YZ plane, the bond will form.


Tom ran into this problem while he was building Re and Si face model 
exercises. At first, I though it was related to the 5 bond carbon that 
he was disposing with a single bond click to the carbonyl, but in trying 
to recreate the problem,  I realized I could create it with a 4 bond 
carbon.


Otis

Otis Rothenberger
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On 12/6/2010 9:54 AM, Robert Hanson wrote:
Hmm. Probably a coding error. You mean when the bond is directly 
vertical on the screen, right?


On Mon, Dec 6, 2010 at 12:44 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

This is random modelkit event, but there is a pattern of sorts: When a
bond is parallel to the screen Y axis, it can sometimes be
impossible to
change bond order by clicking. With hover selection circles
active, you
can see that the selection is not being made. Rotating the model
slightly to destroy the parallel alignment solves the problem. A
carbonyl group seems more susceptible to this than other bonds.

This is obviously not a huge problem, but if anything comes to
mind, let
me know.

Otis

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[Jmol-users] Random Bond Picking Event

2010-12-05 Thread Otis Rothenberger

Bob,

This is random modelkit event, but there is a pattern of sorts: When a 
bond is parallel to the screen Y axis, it can sometimes be impossible to 
change bond order by clicking. With hover selection circles active, you 
can see that the selection is not being made. Rotating the model 
slightly to destroy the parallel alignment solves the problem. A 
carbonyl group seems more susceptible to this than other bonds.

This is obviously not a huge problem, but if anything comes to mind, let 
me know.

Otis

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Re: [Jmol-users] Backslash Confusion

2010-12-01 Thread Otis Rothenberger


Bob,

Thanks again.  Your comments that I'm leaving in this response are a 
good FIND primer for me to keep handy.


Otis

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On 12/2/2010 12:51 AM, Robert Hanson wrote:



On Wed, Dec 1, 2010 at 12:09 PM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

Thanks.  That's what I thought, but because of my uncertainty on
this issue, I was having problems interpreting some find results.
That statement may seem strange, but I have it in my head that the
following logic is correct:

{*}.find("smiles","SOMESMILES") will evaluate true if SOMESMILES
is a non-stereo version of a stereo containing {*}


right.


But not conversely - i.e. "SOMESMILES"
.find("smiles","STRINGEQUIVALENTof{*}SMILES") will evaluate false.

Am I correct on this point?


Sounds right to me. You mean:

"SOMESMILES" .find("smiles","{*}.find("SMILES") )

will be false.

But

"SOMESMILES" .find("smiles","/nostereo/" + "{*}.find("SMILES") )

will return true. "/nostereo/" is a prefix flag that indicates you 
want to ignore any stereochemistry in the string that it precedes. 
Another is "/noaromatic/"



Read

target.find("smiles", test)

as "find test in target" -- if test contains stereochemistry, and 
target does not, then that stereochemistry is not found, and the 
result is false. But if target contains stereochemistry and test does 
not, then it's ok.


In terms of student answers, I think of it as "We are looking for our 
desired answer in the student's work." You want:


studentAnswer.find("SMILES",desiredAnswer)

Note that

  {*}.find("SMILES",{*}.find("SMILES"))

(looking for a model's SMILES string in the model itself) and

  {*}.find("SMILES").find({*}.find("SMILES"))

(looking for a model's SMILES string in itself)

should always return true values, or we have a problem.


Bob

Otis


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Re: [Jmol-users] Backslash Confusion

2010-12-01 Thread Otis Rothenberger


Bob,

Thanks.  That's what I thought, but because of my uncertainty on this 
issue, I was having problems interpreting some find results. That 
statement may seem strange, but I have it in my head that the following 
logic is correct:


{*}.find("smiles","SOMESMILES") will evaluate true if SOMESMILES is a 
non-stereo version of a stereo containing {*}


But not conversely - i.e. "SOMESMILES" 
.find("smiles","STRINGEQUIVALENTof{*}SMILES") will evaluate false.


Am I correct on this point?

Otis


Otis Rothenberger
chemagic.com


On 12/1/2010 12:44 PM, Robert Hanson wrote:

Yes, quite a pain. You'll need  in that case:

JavaScript "C(=C\\C)/C" gets translated to

  C(=\C)/C

which is OK for JavaScript but will be translated again by Jmol to 
. So you want C:


var jsX = "C(=CC)/C"

First escape becomes:

  C(=\\C)/C

which is then properly translated by Jmol as

  C(=\C)/C

This quadruple-slashing only plays a role if you are writing it 
yourself. If you are getting it from some other source, like JME, as a 
string, then you would use:


var smiles = jme.getSmiles()   //[or whatever it is]

var x = jmolEvaluate('{*}.find("smiles"," ' + 
smiles.replace(/\\/g,"") + ' ") ')


for example.

Bob

On Wed, Dec 1, 2010 at 10:13 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

I'm still confused on the use of backslash with find. Here's the
scenario:

sm2 is defined in a jmolScript:

"var sm2 = '" + smileJs1 + "';"

where smilesJs1 is JavaScript string defined as "C(=C\\C)/C"

I want to do a:

{*}.find('SMILES',sm2)

Should my JmolScript string construction be as above or as below?

"var sm2 = '" + smileJs1.replace(/\\/g, '') + "';"

I guess I have the same question about a JME SMILES returned from JME.
You can only see this SMILES displayed. That is to say that you don't
actually the construction of the string in a string definition like
above. The display, of course, shows a single backslash, but what
is it
really in the string?

I thought I had this all under control, but I'm getting some confusing
find results.

Help???

Otis

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[Jmol-users] Backslash Confusion

2010-12-01 Thread Otis Rothenberger

Bob,

I'm still confused on the use of backslash with find. Here's the scenario:

sm2 is defined in a jmolScript:

"var sm2 = '" + smileJs1 + "';"

where smilesJs1 is JavaScript string defined as "C(=C\\C)/C"

I want to do a:

{*}.find('SMILES',sm2)

Should my JmolScript string construction be as above or as below?

"var sm2 = '" + smileJs1.replace(/\\/g, '') + "';"

I guess I have the same question about a JME SMILES returned from JME. 
You can only see this SMILES displayed. That is to say that you don't 
actually the construction of the string in a string definition like 
above. The display, of course, shows a single backslash, but what is it 
really in the string?

I thought I had this all under control, but I'm getting some confusing 
find results.

Help???

Otis

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Re: [Jmol-users] Jmol Variables

2010-11-25 Thread Otis Rothenberger

Rolf,

Print works.

Thanks for the suggestion.

Otis

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> Couldn't you use 'print @foo' instead of the two 'echo' commands,
> avoiding to show something in the Jmol window the user isn't supposed to
> see there anyway? Or is there a problem with 'print' in this context?
>
> Regards,
> Rolf
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Re: [Jmol-users] Jmol Variables

2010-11-25 Thread Otis Rothenberger

Thanks Alexander (and Bob). What a neat trick!

Just for the record, my context was a Jmol variable, etv, that was set 
in a JavaScript loop that used Jmol FIND to locate a SMILES in a 
JavaScript array. A subsequent:

 jmolScriptWait('var foo = etv;'); msg = jmolEvaluate("script('echo 
@foo;echo;')");
 alert(msg);

works beautifully. The second echo is just to make the first echo disappear.

Otis

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On 11/25/2010 4:57 AM, Alexander Rose wrote:
> Hi,
>
> Bob recently showed me you can use script with evaluate, i.e.
>
> jmolScriptWait('var foo = "bar";');
> var msg = jmolEvaluate( "script('echo @foo');" );
> console.log(msg);
>
> this should print 'bar' to your browser console
>
>
> Best
> Alex
>
> - Ursprüngliche Mail -
>> Von: "Otis Rothenberger"
>> An: jmol-users@lists.sourceforge.net
>> Gesendet: Donnerstag, 25. November 2010 07:56:54
>> Betreff: [Jmol-users] Jmol Variables
>> Bob,
>>
>> Are there any Jmol string variable manipulation methods? Specifically,
>> can you calculate the wrap of long echo via script manipulation of the
>> echo string?
>>
>> Actually, a more ideal route would be to pass the Jmol variable to a
>> JavaScript variable and display the information by some JavaScript
>> route. When I do this via a callback function, I have to invoke
>> JavaScript timeouts to work with the JavaScript variable that picked
>> up
>> the Jmol script variable in the callback. If I don't wait a second or
>> two, the JavaScript string is empty. These timeouts can lead to
>> problems, and I'd like to lose them. In your opinion, what's the best
>> way to take a Jmol script variable and pass it to JavaScript for
>> subsequent Web page display, preferably without use of a timeout.
>>
>> Otis
>>
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>>
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[Jmol-users] Jmol Variables

2010-11-24 Thread Otis Rothenberger

Bob,

Are there any Jmol string variable manipulation methods? Specifically, 
can you calculate the wrap of long echo via script manipulation of the 
echo string?

Actually, a more ideal route would be to pass the Jmol variable to a 
JavaScript variable and display the information by some JavaScript 
route. When I do this via a callback function, I have to invoke 
JavaScript timeouts to work with the JavaScript variable that picked up 
the Jmol script variable in the callback. If I don't wait a second or 
two, the JavaScript string is empty. These timeouts can lead to 
problems, and I'd like to lose them. In your opinion, what's the best 
way to take a Jmol script variable and pass it to JavaScript for 
subsequent Web page display, preferably without use of a timeout.

Otis

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Re: [Jmol-users] SMILES Problem

2010-11-23 Thread Otis Rothenberger


Bob,

This is not a huge problem. For what we are doing, we depend mostly on 
internal consistency of our SMILES library, and Jmol SMILES give us 
that. The only place we run into this problem is with a link that 
optimizes a model in the window by making a Resolver call.


Otis

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On 11/23/2010 7:39 AM, Robert Hanson wrote:

Sounds like a resolver issue. This is tricky, but not ambiguous.

C\2=C/C#C

indicates a trans connection ("down" to the other atom at connection 
2; "up" to the triple bond)


More explicitly you would have:

o...@h]1[c@H]/2[C@@]34N[C@@H]5C/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C

but that first "/2" can be just "2" without any ambiguity.

Bob

On Mon, Nov 22, 2010 at 5:14 PM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

I copied Markus with this problem because I don't know if it's a
Resolver of Jmol issue. I think it's a Resolver issue. While I
think the
backslash issue (Jmol to Resolver) is mostly under control, a general
slash issue seems to remain. By way of example:

o...@h]1[c@H]2[C@@]34N[C@@H]5C/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C

In the above example, Resolver gets the .C/C=C\. right, but it
sees the C\2=C/ (cis, I think) as ambiguous. This appears
to be
a general problem when either type of slash precedes a number.

As I type this, I am having a sense of deja vu. This might be an issue
that's already on the table.

Otis

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[Jmol-users] SMILES Problem

2010-11-22 Thread Otis Rothenberger

Bob,

I copied Markus with this problem because I don't know if it's a 
Resolver of Jmol issue. I think it's a Resolver issue. While I think the 
backslash issue (Jmol to Resolver) is mostly under control, a general 
slash issue seems to remain. By way of example:

o...@h]1[c@H]2[C@@]34N[C@@H]5C/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C

In the above example, Resolver gets the .C/C=C\. right, but it 
sees the C\2=C/ (cis, I think) as ambiguous. This appears to be 
a general problem when either type of slash precedes a number.

As I type this, I am having a sense of deja vu. This might be an issue 
that's already on the table.

Otis

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Re: [Jmol-users] Jmol SMILES Questions

2010-11-18 Thread Otis Rothenberger


Bob,

No, I mean with stereo chemistry where D is a priority issue (basic 
organic text problems) Resolver creates the wrong SMILES from a correct 
SMILES query. A correct query from Jmol (re the model in the window) is 
interpreted incorrectly by Resolver. This affects name return, molfile 
return, etc. Resolver gets it exactly backwards I think.


Otis

Otis Rothenberger
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On 11/18/2010 10:51 AM, Robert Hanson wrote:

Shouldn't matter what the group is.

On Thu, Nov 18, 2010 at 9:21 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

Thanks. That fixes it.

As a point of information, I think Resolver gets deuterium
stereochemistry exactly backwards. I'll write Markus about this,
but I want to check myself first.


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Re: [Jmol-users] Jmol SMILES Questions

2010-11-18 Thread Otis Rothenberger


Bob,

Thanks. That fixes it.

As a point of information, I think Resolver gets deuterium 
stereochemistry exactly backwards. I'll write Markus about this, but I 
want to check myself first.


Otis

Otis Rothenberger
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On 11/18/2010 8:45 AM, Robert Hanson wrote:
OK, that's fixed. see 
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip


also not working was any search pattern that involved any sort of H in 
brackets:  C[H], for example, did not match methane


Bob

On Thu, Nov 18, 2010 at 6:22 AM, Robert Hanson <mailto:hans...@stolaf.edu>> wrote:


should be a simple bug fix.


On Wed, Nov 17, 2010 at 10:28 PM, Otis Rothenberger
mailto:osrot...@chemagic.com>> wrote:

Bob,

Jmol SMILES produced [2H] for deuterium, which is correct.
Resolver does
the same. Unfortunately, Jmol Find and Compare don't seem to
be able to
work with this. I'm guessing that a user application side
change would
fix this, but I know you have strong feelings about work
arounds. Two
questions:

1) Is user side replacement of [2H] with [D] prior to a
Compare or Find
a work around in your book?
2) Would it even work? It works for the following for the S
isomer.

var x="br...@h]([D])Br";var y =
x.Find("SMILES","BrC[C@@H](Br)[D]");echo @y

br...@h]([D])Br = Jmol
    BrC[C@@H](Br)[D]") = Resolver

Otis

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[Jmol-users] Jmol SMILES Questions

2010-11-17 Thread Otis Rothenberger

Bob,

Jmol SMILES produced [2H] for deuterium, which is correct. Resolver does 
the same. Unfortunately, Jmol Find and Compare don't seem to be able to 
work with this. I'm guessing that a user application side change would 
fix this, but I know you have strong feelings about work arounds. Two 
questions:

1) Is user side replacement of [2H] with [D] prior to a Compare or Find 
a work around in your book?
2) Would it even work? It works for the following for the S isomer.

var x="br...@h]([D])Br";var y = x.Find("SMILES","BrC[C@@H](Br)[D]");echo @y

br...@h]([D])Br = Jmol
BrC[C@@H](Br)[D]") = Resolver

Otis

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Re: [Jmol-users] Coordination Compound Questions

2010-11-16 Thread Otis Rothenberger


Bob,

OK, I think I get it. To use log capability, I must use the signed applet.

It's about time I set up a signed applet test page anyway. It is, 
indeed, a neat script.


Otis

Otis Rothenberger
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On 11/16/2010 8:38 AM, Robert Hanson wrote:

OK, OK.

Here's a neat script. -- A chiral octahedral compound generator!

It opens $SF6 -- from the NIH CACTVS server, and for 1000 cycles it 
then randomly changes ligands, looking for errors in the algorithm by 
matching the structure to the stereochemical SMILES that Jmol creates 
for it. In addition, it switches chirality and checks to see if those 
are the same. If not, it reports a line that can be used to load that 
chiral compound for inspection. Logs to JmolLog_testSmiles.log


Requires Jmol 12.1.24_dev 
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip


Bob


On Mon, Nov 15, 2010 at 11:53 PM, Robert Hanson <mailto:hans...@stolaf.edu>> wrote:


Otis,

Sure enough -- I forgot about (all trans)-XA2B2C2 and trans-XA2B4.
You would think you wouldn't need @ or @@ for cases like that, but
you do. Even though @ and @@ are the same! Because they still
represent specific stereoisomers, and that is the only way with
SMILES that you can specify the ordering of the bonds around the
central atom. As far as I can tell, the only cases you do NOT need
@ for are XA6, XA5B, and XA5. Even though it is not necessary for
XA5B, it's too much of a trouble to figure out that is what it is,
so I'm just letting Jmol indicate @ for XA5B as well. At least for
now.

Wow, this is really going to be something when the bugs are worked
out! I'll bet you anything this has never been done before.

http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.jar

should take care of that. Please check. Uploading now...


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Re: [Jmol-users] Coordination Compound Questions

2010-11-16 Thread Otis Rothenberger

Bob,

I'm trying to make your script work on a local (served) file. There are 
two file references in your script. I don't understand the second one, 
and I suspect my substitution (below) is causing problems:

 var s = "/*\t"+ i + "\t" + ept + " " + elements[ept] + "\t" + pt + 
"\t" + atoms + "\t" + x + "\t*/\tload ../models/octahedral.txt;

rotate x 20;set echo top left; echo " + i + ";"

What's going on in this variable definition?

Otis

Otis Rothenberger
chemagic.com


On 11/16/2010 8:38 AM, Robert Hanson wrote:
> OK, OK.
>
> Here's a neat script. -- A chiral octahedral compound generator!
>
> It opens $SF6 -- from the NIH CACTVS server, and for 1000 cycles it 
> then randomly changes ligands, looking for errors in the algorithm by 
> matching the structure to the stereochemical SMILES that Jmol creates 
> for it. In addition, it switches chirality and checks to see if those 
> are the same. If not, it reports a line that can be used to load that 
> chiral compound for inspection. Logs to JmolLog_testSmiles.log
>
> Requires Jmol 12.1.24_dev 
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
> Bob
>
>



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Re: [Jmol-users] Coordination Compound Questions

2010-11-15 Thread Otis Rothenberger


Bob,

MA4B2
MA3B3
MA4BC
MA3B2C
MA2B2C2
MA3BCD

All check out. I did not do all possible mismatches, but I did confirm 
all possible matches, as well as the mismatch that existed whenever I 
started a new isomer by changing one model. That leaves 3 classes to go, 
but it's 2:30 AM. Also, Tom gets to do MABCDEF. He just doesn't know it yet.


When I got into this coordination stuff, I tried to find a reference to 
SMILES comparisons. I sure couldn't find a reference. In fact, there was 
disagreement as to how these things should be curated, hence my original 
query to inorganic chemists.


Otis

Otis Rothenberger
chemagic.com


On 11/16/2010 12:53 AM, Robert Hanson wrote:
On Mon, Nov 15, 2010 at 8:28 PM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

After being out all day, I'm back at work. My intent was to begin
a systematic slow trek through all of the octahedral isomer types.
Unfortunately, I did not get far - SX4Y2. It's a strange problem,
so I thought that I better check in with you. By the way, because
of this problem early on, I went back to collecting stddev:

var i = {*}.atomIndex.max + 1;var t = {*}.atomIndex.min;select
within(branch, {atomIndex = i}, {atomIndex=t});var j =
{selected}.find('SMILES');var x = compare({selected}, {not
selected}, @j, 'stddev');echo @x

Call this osrCompare below.

I loaded SF6; I duplicated it in the window to produce two
identical models of SF6: osrCompare ~0 ( 4.5E-8)

I made the trans Br isomer of both: osrCompare = NaN YIKES!

A quick look at the problem:

Original SMILES: [S@@]123456.F6.F1.F2.F3.F4.F5

Duplicated SMILES: [S@@]123456.F6.F1.F2.F3.*F5.F4*

Original SMILES (after Br's): [S@@]123456.F6.Br1.Br2.F3.F4.F5

Duplicated SMILES (after Br's): [S@@]123456.F6.Br1.Br2.F3.*F5.F4*

My duplication method is to do
jmolGetPropertyAsString("extractModel", "all") and then a load APPEND.

In the testing that I did, I never thought to test an obvious
match. I just decided that I should be thorough here.


Otis

Otis Rothenberger
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Re: [Jmol-users] Coordination Compound Questions

2010-11-15 Thread Otis Rothenberger


Bob,

After being out all day, I'm back at work. My intent was to begin a 
systematic slow trek through all of the octahedral isomer types. 
Unfortunately, I did not get far - SX4Y2. It's a strange problem, so I 
thought that I better check in with you. By the way, because of this 
problem early on, I went back to collecting stddev:


var i = {*}.atomIndex.max + 1;var t = {*}.atomIndex.min;select 
within(branch, {atomIndex = i}, {atomIndex=t});var j = 
{selected}.find('SMILES');var x = compare({selected}, {not selected}, 
@j, 'stddev');echo @x


Call this osrCompare below.

I loaded SF6; I duplicated it in the window to produce two identical 
models of SF6: osrCompare ~0 ( 4.5E-8)


I made the trans Br isomer of both: osrCompare = NaN YIKES!

A quick look at the problem:

Original SMILES: [S@@]123456.F6.F1.F2.F3.F4.F5

Duplicated SMILES: [S@@]123456.F6.F1.F2.F3.*F5.F4*

Original SMILES (after Br's): [S@@]123456.F6.Br1.Br2.F3.F4.F5

Duplicated SMILES (after Br's): [S@@]123456.F6.Br1.Br2.F3.*F5.F4*

My duplication method is to do jmolGetPropertyAsString("extractModel", 
"all") and then a load APPEND.


In the testing that I did, I never thought to test an obvious match. I 
just decided that I should be thorough here.


Otis

Otis Rothenberger
chemagic.com


On 11/15/2010 10:19 AM, Otis Rothenberger wrote:

Bob,

For the time being, I'm simply trapping and replacing the responses 
from your Jmol compare/isomer routine when coordination compounds are 
loaded. I can automate this change over in JavaScript. The response 
replacements allow identical/not identical/not same formula responses 
for coordination compounds. This will allow me to do some quick checking.


I've played a bit, and this approach seems to work. Square planar is 
fine. Octahedral will take more testing. I'll get back to you on this.


Otis
Otis Rothenberger
chemagic.com

On 11/15/2010 6:53 AM, Robert Hanson wrote:
Otis, I've also started the same thread at 
<mailto:blueobelisk-smi...@lists.sourceforge.net>>, and I'm hoping it 
can be explained to me how you do this with T-shaped, see-saw, and 
square pyramidal shapes. I think perhaps the answer is going to be 
that you just leave out the missing groups and use explicit [...@tbn] 
or [...@ohn] stereochemical descriptors (and possibly [...@thn] for 
trigonal pyramidal). But I'm not sure about that, because, for example:


[...@oh2]1234.c1.br2.cl3.n4

gives the warning:

WARNING: Chiral center has wrong connectivity -- ignored


at the Daylight Depict site. Hope to hear about that soon.

On Mon, Nov 15, 2010 at 12:44 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

I think I see it. If I'm analyzing @ or @@, group 1 is toward me.
Is that correct?

Yes, group 1 is toward you, and the rotation about the others is the 
same as depicted in the @ symbol itself -- CCW for "@" . The first 
and last groups must be axial. The ones in between are the ones that 
are checked for rotation order.


Notice that the way this works for SMILES generation in Jmol is that 
Jmol will now first list all "components" based on atoms that have 
more than four attachments. For example, a particular isomer of 
SF3IBrCl might be:


[...@]123456.i5.f1.br6.f4.f3.cl2

and a ferrocene model I have returns:

[fe]123456789%10...@h]1%11[c@h]...@h]4[c@H]3[C@@h]%112...@h]6%12[c@h]%1...@h]9[c@h]...@h]7%12 



That is, we're creating a "generic" n-coordinate center and then just 
listing the attached components. The nice thing about this is that 
there's no significance to the order of groups in the individual 
components -- it's just the connection numbers 1-10 that determines 
the stereochemistry, and you can have as many of these connected 
inorganic components as you need to get the job done.


The success here is based on not requiring any sort of "canonical" or 
"unique" SMILES description for our purposes. Jmol can match 
structures to stereochemical SMILES strings as well as stereochemical 
SMILES strings to stereochemical SMILES strings without any need for 
canonicalization. So that's all we need.


Except for your finding a bug possibly, Jmol should now be able to 
match any stereochemical SMILES involving allenyl, tetrahedral, 
trigonal bipyramidal, or octahedral stereochemistry descriptors, and 
it will generate stereochemical SMILES strings for structures with 
all of these shapes automatically.


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Re: [Jmol-users] Coordination Compound Questions

2010-11-15 Thread Otis Rothenberger

Bob,

For the time being, I'm simply trapping and replacing the responses from
your Jmol compare/isomer routine when coordination compounds are loaded.
I can automate this change over in JavaScript. The response replacements
allow identical/not identical/not same formula responses for
coordination compounds. This will allow me to do some quick checking.

I've played a bit, and this approach seems to work. Square planar is
fine. Octahedral will take more testing. I'll get back to you on this.

Otis

Otis Rothenberger
chemagic.com

On 11/15/2010 6:53 AM, Robert Hanson wrote:
Otis, I've also started the same thread at
<mailto:blueobelisk-smi...@lists.sourceforge.net>>, and I'm hoping it
can be explained to me how you do this with T-shaped, see-saw, and
square pyramidal shapes. I think perhaps the answer is going to be
that you just leave out the missing groups and use explicit [...@tbn]
or [...@ohn] stereochemical descriptors (and possibly [...@thn] for
trigonal pyramidal). But I'm not sure about that, because, for example:

[...@oh2]1234.c1.br2.cl3.n4

gives the warning:

WARNING: Chiral center has wrong connectivity -- ignored

at the Daylight Depict site. Hope to hear about that soon.

On Mon, Nov 15, 2010 at 12:44 AM, Otis Rothenberger
mailto:osrot...@chemagic.com>> wrote:

Bob,

I think I see it. If I'm analyzing @ or @@, group 1 is toward me.
Is that correct?

Yes, group 1 is toward you, and the rotation about the others is the
same as depicted in the @ symbol itself -- CCW for "@" . The first and
last groups must be axial. The ones in between are the ones that are
checked for rotation order.

Notice that the way this works for SMILES generation in Jmol is that
Jmol will now first list all "components" based on atoms that have
more than four attachments. For example, a particular isomer of
SF3IBrCl might be:

[...@]123456.i5.f1.br6.f4.f3.cl2

and a ferrocene model I have returns:

[fe]123456789%10...@h]1%11[c@h]...@h]4[c@H]3[C@@h]%112...@h]6%12[c@h]%1...@h]9[c@h]...@h]7%12

That is, we're creating a "generic" n-coordinate center and then just
listing the attached components. The nice thing about this is that
there's no significance to the order of groups in the individual
components -- it's just the connection numbers 1-10 that determines
the stereochemistry, and you can have as many of these connected
inorganic components as you need to get the job done.

The success here is based on not requiring any sort of "canonical" or
"unique" SMILES description for our purposes. Jmol can match
structures to stereochemical SMILES strings as well as stereochemical
SMILES strings to stereochemical SMILES strings without any need for
canonicalization. So that's all we need.

Except for your finding a bug possibly, Jmol should now be able to
match any stereochemical SMILES involving allenyl, tetrahedral,
trigonal bipyramidal, or octahedral stereochemistry descriptors, and
it will generate stereochemical SMILES strings for structures with all
of these shapes automatically.

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Re: [Jmol-users] Coordination Compound Questions

2010-11-14 Thread Otis Rothenberger


Bob,

I think I see it. If I'm analyzing @ or @@, group 1 is toward me. Is 
that correct?


I'm playing around with two octahedral models and

var x = compare({selected}, {not selected}, @j, 'stddev')

where @j is the selected SMILES.

Matches look good. What model characteristics would lead to a correct 
non-match of a say 0.2ish vs NaN - same stoichiometric formula. I'm not 
seeing a pattern.


I do see the auto SMILES update. This time I just used the link commands 
that I have set up for model kit mode. It also auto updates on an sp3 
invert click. Neat.


The "database" that we are setting up was simply a .js JSON structure. 
The size got way out of hand, so I moved it to the server side and  
write JSON from it as needed. I can see that I have some SMILES to 
change in the database in light of some of the things you've been doing.


Otis

Otis Rothenberger
chemagic.com


On 11/14/2010 11:32 PM, Robert Hanson wrote:
One correction. I had Jmol generating octahedral stereochemistry only 
if two or more trans pairs are identical. While those cases don't need 
@ or @@, one more case is like that as well -- when three of the four 
groups that are not listed first or last are identical. Also, I was 
forgetting that even if we don't need @ or @@, we still need to get 
the first and last groups to be axially related.


Hurray for the SMILES "." convention!!! (Which makes this all possible.)

This should be fixed now:

http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

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Re: [Jmol-users] Coordination Compound Questions

2010-11-14 Thread Otis Rothenberger


Bob,

I  don't know if I hit all possible combinations, but I can't break the 
trans SMILES listing. This is great.


I don't see the auto update. This could be related to my own message 
callbacks. I don't even see SMILES changes on find unless I do atom 
substitutions - as opposed to drags. As a said above, this seems to work 
perfectly. Since this is my main concern (atom substitution), I'm a 
happy camper. The drag/SMILES change sounds like great fun, however.


Otis

Otis Rothenberger
chemagic.com


On 11/14/2010 3:17 PM, Robert Hanson wrote:
Otis, I have something for you. Woke up this morning with an idea, and 
it appears to have worked. Jmol now generates correct stereochemical 
SMILES for trigonal bipyramidal and octahedral shapes. Odd that 
Daylight didn't consider T-shaped and square pyramidal. Oh well! This 
is still better than nothing, I think. The trick was in getting Jmol 
to list the ligands in the proper order -- first a trans-pair, then 
the others in the correct order.


http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

Anyway, please test. A simple way to do that is to use

LOAD http://chemapps.stolaf.edu/jmol/docs/examples-11/data/SF6.smol 
-1  # just the first vibration

wireframe only;label

{atomno=3}.element = "Br"
{atomno=5}.element = "I"
{atomno=6}.element = "Cl"
x = {*}.find("SMILES")
print x
print {*}.find("SMILES",x)

# and variations on that theme. Also, this is sort of fun:

set modelkitmode
delete atomIndex=6
set picking dragAtom
set echo top left
echo @{ {*}.find("SMILES")}

# now drag atoms around and watch the top left echo update automatically!


Bob

On Fri, Nov 12, 2010 at 9:39 AM, Robert Hanson <mailto:hans...@stolaf.edu>> wrote:




On Fri, Nov 12, 2010 at 9:22 AM, Otis Rothenberger
mailto:osrot...@chemagic.com>> wrote:

Bob,

Thanks for the quick repair job!

Follow-up question: By my testing, the SPn SMILES notation allows
complete FIND/compare ability for simple square planar
complexes. Does
the order of the ligands in the octahedral SMILES carry the
same punch?
I've had success with simple tests, but there's a lot more to
test here,
so I though I'd go directly to the SMILES master.


There are two kinds of finds:

A) {structure}.find("SMILES", smilesString)

B) smilesString1.find("SMILES", smilesString2)

for (A), all stereochemical notation is implemented -- allenyl,
tetrahedral, square planar, trigonal bipyramidal, and octahedral.

for (B), allenyl, tetrahedral, and square planar are fully
implemented. Trigonal bipyramidal requires that the two axial
ligands be listed first and last; in the case of octahedral, we
require that the two designated "axial" groups be listed first and
last.

No reason for this other that I did not finish the job and have no
access to the unpublished supposed additional @OHn and @TBn
designations. I think I could easily enough implement octahedral
checking as long as any two diametrically opposed groups are given
first and last.

Not 100% sure I can get Jmol to produce accurate SMILES for *any*
octahedral or trigonal bipyramidal compound.


Bob

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Re: [Jmol-users] Coordination Compound Questions

2010-11-12 Thread Otis Rothenberger

All,

I apologize for packing two questions in one chain, but now that it's 
done, I don't want to break chain.

As an organic chemist, I got dragged into this coordination compound 
issue kicking and screaming - "So it goes." Here's a blog that uses 
ferrocene in PubChem as an example of the problem:

http://depth-first.com/articles/2006/12/12/the-problem-with-ferrocene/

I'd still value any opinions on how this should be handled in the Jmol 
sandbox. The thing that suddenly makes establishing some standard an 
issue is the recent inclusion of SMILES and model editing into the power 
tool kit of Jmol.

Otis

Otis Rothenberger
chemagic.com


On 11/11/2010 8:37 PM, Otis Rothenberger wrote:
> All-
>
> I'm looking for some advice from inorganic chemists (or others) on the 
> subject of appropriate molfiles for coordination compounds. To put the 
> question in perspective, we are assembling a database of organic 
> compounds found in  standard organic text. This list will, of course, 
> include some coordination compounds. The database will include, _A_ 
> SMILES that Jmol creates for the model, _THE_ unique SMILES  that NIH 
> Resolver creates, a common name, the IUPAC name, and a hook to the 
> molfile.
>
> It is the SMILES & molfile that present a problem for coordination 
> compounds. What is the standard (if any exists) for creating 
> coordinate bonds in a molfile? It appears that a common approach is to 
> not show bonds at all (PubChem and Emolecules seem to do this for 
> example), with the resulting SMILES being a multi-structure SMILES. 
> For our purpose, a single bound geometry retaining entity is 
> preferred. We can create the unconnected model in Spartan, and then 
> append/edit the molfile connection table to show coordinate bonds. Is 
> there a preference or some standard for the molfiles of these 
> compounds? Single, partial, unidentified are among the molefile options.
>
> Bob is the master of Jmol SMILES, so I'll direct the second question 
> to him.
>
> The SMILES on these compounds present another problem in Jmol. By way 
> of example,  if we construct an unconnected ferrocene in SPARTAN and 
> then edit the molfile connection table so that the cyclopentadienyl 
> anion carbons are assigned "aromatic" and the coordinate bonds to iron 
> are assigned as type 8 ("any", evidently interpreted by Jmol as 
> partial ), then we get the following SMILES from Jmol:
>
> [...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@@H]5[C@@h]...@h]23
>  
>
>
> The NIH Resolver reads this and returns evidence that it understands 
> the bond connections - correctly connected 2D molfile and correctly 
> connected GIF image. This appears to be a correct SMILES for the 
> ferrocene that we constructed. It appears that the SMILES is very 
> confused about the geometry of the cylopentadienyl anion hydrogens, 
> but the connections are correct.
>
> Unfortunately, Jmol does not seem to recognize what it created. With 
> the same model in the Jmol window, the following :
>
> var x = 
> "[...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@@H]5[C@@h]...@h]23";
>  
> var y = {*}.find("SMILES",x);echo @y
>
> does not produce a match. Resolver will also produce a unique SMILES 
> from Jmol's SMILES:
>
> [...@h]12[c@@H]3[C@@H]4[C@@h]...@h]1[fe]23456789[c@H]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10
>  
>
>
> The following SMILES Find (Resolver in Jmol) is a perfect match:
>
> var x = 
> "[...@h]12[c@@H]3[C@@H]4[C@@h]...@h]1[fe]23456789[c@H]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10";
>  
> var y = {*}.find("SMILES",x);echo @y
>
> Help!
>
> Otis
>



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Re: [Jmol-users] Coordination Compound Questions

2010-11-12 Thread Otis Rothenberger


Bob,

I think "A" is all I need." Everything we do is based on issues related 
to the model in the Jmol window (I think? See below). This involves 
queries to a number of resources (check name, check image, get remote db 
molfile, check FIND in database SMILES vs model SMILES... ), but the 
query is always based on the SMILES generated by the model in the Jmol 
window.


With two models in the window, I'm using the following logic:

string for selected atoms in model 1.find("SMILES",string for selected 
atoms in model 2)


To make that truly method A, do I need to change to:

{selected atoms in model 1}.find("SMILES",string for selected atoms in 
model 2)


???

Do you mean that you think you can actually detect cis/trans and 
enatiomers in octahedral systems?


Otis

Otis Rothenberger
chemagic.com


On 11/12/2010 10:39 AM, Robert Hanson wrote:



On Fri, Nov 12, 2010 at 9:22 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

Thanks for the quick repair job!

Follow-up question: By my testing, the SPn SMILES notation allows
complete FIND/compare ability for simple square planar complexes. Does
the order of the ligands in the octahedral SMILES carry the same
punch?
I've had success with simple tests, but there's a lot more to test
here,
so I though I'd go directly to the SMILES master.


There are two kinds of finds:

A) {structure}.find("SMILES", smilesString)

B) smilesString1.find("SMILES", smilesString2)

for (A), all stereochemical notation is implemented -- allenyl, 
tetrahedral, square planar, trigonal bipyramidal, and octahedral.


for (B), allenyl, tetrahedral, and square planar are fully 
implemented. Trigonal bipyramidal requires that the two axial ligands 
be listed first and last; in the case of octahedral, we require that 
the two designated "axial" groups be listed first and last.


No reason for this other that I did not finish the job and have no 
access to the unpublished supposed additional @OHn and @TBn 
designations. I think I could easily enough implement octahedral 
checking as long as any two diametrically opposed groups are given 
first and last.


Not 100% sure I can get Jmol to produce accurate SMILES for *any* 
octahedral or trigonal bipyramidal compound.



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Re: [Jmol-users] Coordination Compound Questions

2010-11-12 Thread Otis Rothenberger

Bob,

Thanks for the quick repair job!

Follow-up question: By my testing, the SPn SMILES notation allows 
complete FIND/compare ability for simple square planar complexes. Does 
the order of the ligands in the octahedral SMILES carry the same punch? 
I've had success with simple tests, but there's a lot more to test here, 
so I though I'd go directly to the SMILES master.

Markus (Resolver) wrote  several weeks ago indicating that the Resolver 
SMILES are only internally unique. He mentioned that Daylight never 
released their algorithm. I'm carrying them in our data base with the 
hope that in our mini-internal system I can use them to pick up isomer 
types in coordination complexes. This would not be a general algorithm, 
but it would allow detecting isomer types in our database for problem 
exercises.

Otis

Otis Rothenberger
chemagic.com

On 11/12/2010 7:50 AM, Robert Hanson wrote:
> Ah, HA! Found it. It was in the SMILES reader translating indicated 
> stereochemistry to actual 3D positions when a new component mark "." 
> was followed by a stereochemistry indicator with H, "[...@h]", which was 
> followed immediately with the SECOND ring bond connection number. Wow. 
> That's obscure. One little line in the code Amazing. Good test, Otis!
>
> version=12.1.22_dev
>
> # bug fix: SMILES matching string with "@h]1" reads stereochemistry 
> incorrectly
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
>
>

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[Jmol-users] Coordination Compound Questions

2010-11-11 Thread Otis Rothenberger

All-

I'm looking for some advice from inorganic chemists (or others) on the 
subject of appropriate molfiles for coordination compounds. To put the 
question in perspective, we are assembling a database of organic 
compounds found in  standard organic text. This list will, of course, 
include some coordination compounds. The database will include, _A_ 
SMILES that Jmol creates for the model, _THE_ unique SMILES  that NIH 
Resolver creates, a common name, the IUPAC name, and a hook to the molfile.

It is the SMILES & molfile that present a problem for coordination 
compounds. What is the standard (if any exists) for creating coordinate 
bonds in a molfile? It appears that a common approach is to not show 
bonds at all (PubChem and Emolecules seem to do this for example), with 
the resulting SMILES being a multi-structure SMILES. For our purpose, a 
single bound geometry retaining entity is preferred. We can create the 
unconnected model in Spartan, and then append/edit the molfile 
connection table to show coordinate bonds. Is there a preference or some 
standard for the molfiles of these compounds? Single, partial, 
unidentified are among the molefile options.

Bob is the master of Jmol SMILES, so I'll direct the second question to him.

The SMILES on these compounds present another problem in Jmol. By way of 
example,  if we construct an unconnected ferrocene in SPARTAN and then 
edit the molfile connection table so that the cyclopentadienyl anion 
carbons are assigned "aromatic" and the coordinate bonds to iron are 
assigned as type 8 ("any", evidently interpreted by Jmol as partial ), 
then we get the following SMILES from Jmol:

[...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@@H]5[C@@h]...@h]23

The NIH Resolver reads this and returns evidence that it understands the 
bond connections - correctly connected 2D molfile and correctly 
connected GIF image. This appears to be a correct SMILES for the 
ferrocene that we constructed. It appears that the SMILES is very 
confused about the geometry of the cylopentadienyl anion hydrogens, but 
the connections are correct.

Unfortunately, Jmol does not seem to recognize what it created. With the 
same model in the Jmol window, the following :

var x = 
"[...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@@H]5[C@@h]...@h]23";
 
var y = {*}.find("SMILES",x);echo @y

does not produce a match. Resolver will also produce a unique SMILES 
from Jmol's SMILES:

[...@h]12[c@@H]3[C@@H]4[C@@h]...@h]1[fe]23456789[c@H]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10

The following SMILES Find (Resolver in Jmol) is a perfect match:

var x = 
"[...@h]12[c@@H]3[C@@H]4[C@@h]...@h]1[fe]23456789[c@H]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10";
 
var y = {*}.find("SMILES",x);echo @y

Help!

Otis

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Re: [Jmol-users] Jmol SMILES problem


Grrr...

Isoprene was another hand editing issue. I had:

"smiJ": "C/C/1=C.C\1=C", "smiR": "CC(=C)C=C",

It should have been:

"smiJ": "C/C/1=C.C\\1=C", "smiR": "CC(=C)C=C",

The smiles strings are handed to Jmol script via JavaScript, so the 
database has to store \\ for \.


I now have Jmol script automatically creating the correct database 
entries, but I have 300 of these that predate this approach.  I'm trying 
to clean this up by hand.


SmiR is unique, but I want a Jmol SMILES reference in the database. 
That's the reason for the two entries.


Otis



Otis Rothenberger
chemagic.com


On 11/9/2010 12:35 PM, Robert Hanson wrote:

what's with the lower case (c=O)?

On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

I think the following are two correct SMILES for 3-methyl
benzaldehyde:

c12=cc=cc(C)=c2.C1=O

c1(c=O)=cc=cc(C)=c1

With the first being generated by the current model window and the
second coming from a database, the following fails:

var cks = {*}.find('SMILES','c1(c=O)=cc=cc(C)=c1');echo @cks

The following, of course, does not fail:

var cks = {*}.find('SMILES','c12=cc=cc(C)=c2.C1=O');echo @cks

Without giving the data here, I have a reciprocal case (failure) with
isoprene - i.e. the dot notation is in the database and the current
model is producing a non-dot SMILES.

Is this just a fact of life with the dot notation, or is this a
correctable problem? By the way, Resolver reads all of this just fine.
My problem is making my local database check the model in the window
using Jmol script.

One more question, probably naive: With the FIND that worked above, I
was surprised by the result:

{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}

I take it that the elements and the "=" are being matched (found)
- not
the dot??

Otis

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Re: [Jmol-users] Jmol SMILES problem


Bob,

That's clearly my mistake. A lot of the kekule aromatic entries in my 
database came from JME, and I hand edited JME's upper case aromatic "C" 
to lower case aromatic "c" for Jmol comparison. I clearly hand edited a 
non-aromatic here. I'll check the isoprene again to see if there is 
anything obvious.


Otis

Otis Rothenberger
chemagic.com


On 11/9/2010 12:35 PM, Robert Hanson wrote:

what's with the lower case (c=O)?

On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

I think the following are two correct SMILES for 3-methyl
benzaldehyde:

c12=cc=cc(C)=c2.C1=O

c1(c=O)=cc=cc(C)=c1

With the first being generated by the current model window and the
second coming from a database, the following fails:

var cks = {*}.find('SMILES','c1(c=O)=cc=cc(C)=c1');echo @cks

The following, of course, does not fail:

var cks = {*}.find('SMILES','c12=cc=cc(C)=c2.C1=O');echo @cks

Without giving the data here, I have a reciprocal case (failure) with
isoprene - i.e. the dot notation is in the database and the current
model is producing a non-dot SMILES.

Is this just a fact of life with the dot notation, or is this a
correctable problem? By the way, Resolver reads all of this just fine.
My problem is making my local database check the model in the window
using Jmol script.

One more question, probably naive: With the FIND that worked above, I
was surprised by the result:

{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}

I take it that the elements and the "=" are being matched (found)
- not
the dot??

Otis

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[Jmol-users] Jmol SMILES problem

Bob,

I think the following are two correct SMILES for 3-methyl benzaldehyde:

c12=cc=cc(C)=c2.C1=O

c1(c=O)=cc=cc(C)=c1

With the first being generated by the current model window and the 
second coming from a database, the following fails:

var cks = {*}.find('SMILES','c1(c=O)=cc=cc(C)=c1');echo @cks

The following, of course, does not fail:

var cks = {*}.find('SMILES','c12=cc=cc(C)=c2.C1=O');echo @cks

Without giving the data here, I have a reciprocal case (failure) with 
isoprene - i.e. the dot notation is in the database and the current 
model is producing a non-dot SMILES.

Is this just a fact of life with the dot notation, or is this a 
correctable problem? By the way, Resolver reads all of this just fine. 
My problem is making my local database check the model in the window 
using Jmol script.

One more question, probably naive: With the FIND that worked above, I 
was surprised by the result:

{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}

I take it that the elements and the "=" are being matched (found) - not 
the dot??

Otis

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Re: [Jmol-users] rotate selected atoms using the mouse

Alex,

Yeah, that is the "icky" case. PLM is bonded to the protein chain. You 
can break that sulfur bond and then play with PLM independently (using 
model kit mode). You can also rotate it about that bond (using model kit 
mode). For complete independent movement while attached, Bob obviously 
has a plan! Bob, what's that sulfur bond going to do during the movement?

Otis

Otis Rothenberger
chemagic.com

On 11/9/2010 7:23 AM, Robert Hanson wrote:

Alex,

That's what I needed. We will need a new parameter:

set rotateSelectedAtoms

It will be in Jmol 12.1.21, to be released later today.

Bob

On Tue, Nov 9, 2010 at 4:20 AM, Alexander Rose 
mailto:alexander.r...@weirdbyte.de>> wrote:

Hi,

thanks for your efforts Otis! What I want is not as fancy as Bob
guessed. Let me try to reformulate what I want to achieve: "Use
the mouse to rotate an arbitrary set of atoms around its geometric
center.".

I set up a page with some comments (also attached below) to
clarify things, hopefully:
http://weirdbyte.de/jmol-test/html/move.html

Alex

// comments from the website

load "../data/3cap.pdb"; set selectionHalos ON; select chain=a;
set dragSelected ON; set allowRotateSelected ON;
Rotating (alt-left) and translating (alft-shift-left) of selected
chain a works fine, only selected atoms are moved. This is what I
want in general, a way to move (rotate, translate) only selected
atoms using the mouse, but depending on bonding, I have not found
a way to achive it (for translating I got it, but not for
rotating) as I hope to show below

load "../data/3cap.pdb"; set selectionHalos ON; select chain=a and
plm; set dragSelected ON; set allowRotateSelected ON;
Translating (alt-shift-left) works as expected, moves just the
selected atoms (plm). Rotating (alt-left) moves plm and the bond
protein chain=a, this works as documented "set allowRotateSelected
FALSE - When set TRUE, this parameter allows user rotation of the
molecule containing the selected atom using the mouse (holding ALT
down while dragging). The coordinates of the rotated molecule will
be sightly degraded in this process." However, I am looking for a
way to just rotate the selected plm, regardless of weather it is
bond to the protein chain a.

load "../data/3cap.pdb"; set selectionHalos ON; select chain=a and
plm; set picking dragMolecule;
The picking/drag approach, selection does not matter. Pick/drag
the protein chain a moves just the protein chain a. Pick/drag plm
moves the protein chain a and all bond non protein molecules,
including plm. This is asymmetric, is there a rationale for that?
Actually I do not mind, I just want a way to move (rotate,
translate) only selected atoms using the mouse.

- Ursprüngliche Mail -
> Von: "Otis Rothenberger" mailto:osrot...@chemagic.com>>
> An: jmol-users@lists.sourceforge.net
<mailto:jmol-users@lists.sourceforge.net>
> Gesendet: Dienstag, 9. November 2010 06:06:00
> Betreff: Re: [Jmol-users] rotate selected atoms using the mouse
> Hi Alexander and Bob-
>
> I'm going to go out on a limb here and say that I think Alexander
> wants to do something that's not as complex as it seems. While my
> description below uses the links on my page, I am really just using
> Jmol's model kit mode commands.
>
> I'll use lactose permease (courtesy of RPI) as an example. Go to:
>
> http://chemagic.com/web_molecules/script_page_large.aspx
>
> 1) Click to go to the Model Tools
> 2) From the MM Load menu, select  - so named to bring it to the
> top of the menu
>
> The above is lactose permease (two actually because of the crystal
> structure data) with a galactospyranoside "dimer" substrate tucked
> inside.
>
> 3) Click the Edit link to go to the edit menu.
> 4) Click the Model "move" link and the Bonds picking "off" link.
>
> The above selects the move mode that we need below.
Additionally, both
> clicks together turn off bond and atom editing. For a model this
> large, you don't want to see what happens on an accidental edit!
>
> 5) In the script command field, enter "set selectHetero on;select
> hetero;color pink" and click Run (No Quotes in the Actual Command).
>
> OK, there's your tiny substrate. Substrates really because of
the two
> proteins.
>
> 6) Zoom in until you are sure that you can get a clean click on
a pink
> substrate atom.
>
> 7) Shift-Click-Drag to rotate any way you want with respect to the
> prote

Re: [Jmol-users] rotate selected atoms using the mouse

Oh my. I had forgotten about this. If you actually open Bob's Jmol model 
kit mode, turn the substrate pink:


set modelKitMode;set selectHetero on;select hetero;color pink

and use the drag (shift to rotate) commands to move the substrate 
slightly out of place, then the drag/minimize command will simulate 
docking back into place.


I just love this thing!

Otis

Otis Rothenberger
chemagic.com


On 11/9/2010 12:06 AM, Otis Rothenberger wrote:

Hi Alexander and Bob-

I'm going to go out on a limb here and say that I think Alexander 
wants to do something that's not as complex as it seems. While my 
description below uses the links on my page, I am really just using 
Jmol's model kit mode commands.


I'll use lactose permease (courtesy of RPI) as an example. Go to:

http://chemagic.com/web_molecules/script_page_large.aspx

1) Click to go to the Model Tools
2) From the MM Load menu, select  - so named to bring it to the 
top of the menu


The above is lactose permease (two actually because of the crystal 
structure data) with a galactospyranoside "dimer" substrate tucked inside.


3) Click the Edit link to go to the edit menu.
4) Click the Model "move" link and the Bonds picking "off" link.

The above selects the move mode that we need below. Additionally, both 
clicks together turn off bond and atom editing. For a model this 
large, you don't want to see what happens on an accidental edit!


5) In the script command field, enter "set selectHetero on;select 
hetero;color pink" and click Run (No Quotes in the Actual Command).


OK, there's your tiny substrate. Substrates really because of the two 
proteins.


6) Zoom in until you are sure that you can get a clean click on a pink 
substrate atom.


7) Shift-Click-Drag to rotate any way you want with respect to the 
protein. OR Click-Drag to move the substrate in the XY plane of the 
screen.


Alexander, is this analogous to what you want to do?

Note: If that substrate is bound in there, then things get icky. Your 
going to end up with the connected bond stretching like a taffy pull. 
In this case, however, the substrate is a separate entity.


I hope I'm on the right track here and not wasting your time!

Otis


Otis Rothenberger
chemagic.com


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Re: [Jmol-users] rotate selected atoms using the mouse


Hi Alexander and Bob-

I'm going to go out on a limb here and say that I think Alexander wants 
to do something that's not as complex as it seems. While my description 
below uses the links on my page, I am really just using Jmol's model kit 
mode commands.


I'll use lactose permease (courtesy of RPI) as an example. Go to:

http://chemagic.com/web_molecules/script_page_large.aspx

1) Click to go to the Model Tools
2) From the MM Load menu, select  - so named to bring it to the top 
of the menu


The above is lactose permease (two actually because of the crystal 
structure data) with a galactospyranoside "dimer" substrate tucked inside.


3) Click the Edit link to go to the edit menu.
4) Click the Model "move" link and the Bonds picking "off" link.

The above selects the move mode that we need below. Additionally, both 
clicks together turn off bond and atom editing. For a model this large, 
you don't want to see what happens on an accidental edit!


5) In the script command field, enter "set selectHetero on;select 
hetero;color pink" and click Run (No Quotes in the Actual Command).


OK, there's your tiny substrate. Substrates really because of the two 
proteins.


6) Zoom in until you are sure that you can get a clean click on a pink 
substrate atom.


7) Shift-Click-Drag to rotate any way you want with respect to the 
protein. OR Click-Drag to move the substrate in the XY plane of the screen.


Alexander, is this analogous to what you want to do?

Note: If that substrate is bound in there, then things get icky. Your 
going to end up with the connected bond stretching like a taffy pull. In 
this case, however, the substrate is a separate entity.


I hope I'm on the right track here and not wasting your time!

Otis


Otis Rothenberger
chemagic.com


On 11/8/2010 4:12 PM, Robert Hanson wrote:
That's going to rotate the atoms about a specific molecular axis. Do 
you want it to rotate about a specific window axis, regardless of how 
the model is oriented? Is that the problem? There might be a way of 
doing that with quaternions.



On Mon, Nov 8, 2010 at 12:39 PM, Alexander Rose 
mailto:alexander.r...@weirdbyte.de>> wrote:


Hi,

>From the manual

"set allowRotateSelected FALSE

When set TRUE, this parameter allows user rotation of the molecule
containing the selected atom using the mouse (holding ALT down
while dragging). The coordinates of the rotated molecule will be
sightly degraded in this process."


I would like to rotate an arbitrary set of atoms using the mouse
and currently "set allowRotateSelected TRUE" is the closest thing
I found, but works only for a single complete molecule.

I started to implement something myself using bind and
rotateSelected and in principle it works:

bind "CTRL-ALT-LEFT" "rotateSelected axisangle {1 1 1 _DELTAX}"

but its not quite as "set allowRotateSelected TRUE". I think I
need to make the rotation angle depended on the current view?! Any
suggestions?


Best
Alexander


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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.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


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Re: [Jmol-users] rotate selected atoms using the mouse


Alexander,

I'm still a little confused about your objective. Try this. Go to:

http://chemagic.com/web_molecules/script_page_large.aspx

Click the Molecular Editor link. Click "duplicate." There are now two 
models in the window. Click "move." After you click "move," either model 
can be click/dragged (translated) to any position in the window. If you 
hold down the shift key, the model will rotate rather than translate. Is 
that what you want?


I should mention that you can drag individual atoms. The command "set 
picking dragAtom" will allow you to do this. The "drag" link on my page 
above will do the same thing. After you click the "drag" link, you can 
click-drag individual atoms within a model - i.e. sculpt the model one 
atom at a time. Is that what you would like to do, albeit several atoms 
rather than just one?


Otis

Otis Rothenberger
chemagic.com


On 11/8/2010 3:19 PM, Alexander Rose wrote:

Hi Otis,

Am 08.11.2010 um 20:22 schrieb Otis Rothenberger:


Hi Alexander-

I'm not sure exactly what you want to do, but if you want to
independently translate or rotate non-bonded models, or rotate about a
given bond (i.e. conformation rotation), then there is a really simple
way to do either of these.

1) With one or more models in the same window, the command "set picking
dragMolecule" will allow you to click/drag the models independently.
Shift/click/drag will allow independent rotation.


(dragMolecule is missing from the documentation)

Anyway it works fine and smooth for _molecules_, not for some atom 
selection. I want to use it (and have) to work with proteins. For 
example to align a dimer (two molecules) with a lipid bilayer patch.


Whenever there are multiple molecules involved, the majority of 
existing functions offer no easy solutions. "set dragSelected ON" does 
work for translating all selected atoms, regardless weather they are 
from one or more molecules.


Alex

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Re: [Jmol-users] rotate selected atoms using the mouse

Hi Alexander-

I'm not sure exactly what you want to do, but if you want to 
independently translate or rotate non-bonded models, or rotate about a 
given bond (i.e. conformation rotation), then there is a really simple 
way to do either of these.

1) With one or more models in the same window, the command "set picking 
dragMolecule" will allow you to click/drag the models independently.  
Shift/click/drag will allow independent rotation.

2) The command "set picking rotateBond" will allow you to click select a 
bond. After the bond is click selected, shift/click/drag on either side 
of the bond will do a conformation rotation.

Alternatively, you can enter Jmol's mode lkit mode and do all of this 
via menus - right-click/computaion/model kit.

Otis

Otis Rothenberger
chemagic.com


On 11/8/2010 1:39 PM, Alexander Rose wrote:
> Hi,
>
> > From the manual
>
> "set allowRotateSelected FALSE
>
> When set TRUE, this parameter allows user rotation of the molecule containing 
> the selected atom using the mouse (holding ALT down while dragging). The 
> coordinates of the rotated molecule will be sightly degraded in this process."
>
>
> I would like to rotate an arbitrary set of atoms using the mouse and 
> currently "set allowRotateSelected TRUE" is the closest thing I found, but 
> works only for a single complete molecule.
>
> I started to implement something myself using bind and rotateSelected and in 
> principle it works:
>
> bind "CTRL-ALT-LEFT" "rotateSelected axisangle {1 1 1 _DELTAX}"
>
> but its not quite as "set allowRotateSelected TRUE". I think I need to make 
> the rotation angle depended on the current view?! Any suggestions?
>
>
> Best
> Alexander
>
> --
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



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Re: [Jmol-users] Java security: mix of unsigned and signed content

Angel, et al-

I don't know if this is relevant, but when I had the problem with 
1.6.0_22, I saw a number of blogs, including one at Oracle, that 
indicated a cookie problem related to security and 1.6.0_22. I was in a 
hurry trying to track down a Jmol issue, so I did not want to take the 
time to mess with Oracle and 1.6.0_22. I just backed of to 1.6.0_21.

I should note that my security problem with 1.6.0_22 was with the 
unsigned applet. I should also note that the files were being served, 
not loaded via local directory path. This was not a typical local 
problem associated with an attempt to load a molfile via a local path. 
My local server should have served those files without the security 
violation. Jmol under 1.6.0_22 was not allowed to load them - under 
1.6.0_21, all was well.

Otis

Otis Rothenberger
chemagic.com

On 11/8/2010 10:39 AM, Angel Herráez wrote:
> Might be something with my system, but I am seeing it at both
> computers, and with different applets (Jmol unsigned, my campus
> Blackboard environment, among others). Also in different browsers.
>
> The warning jumps most often saying it's jmolApplet0.jar, but some
> times it has been another component. Might it be the localization
> module?
>

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Re: [Jmol-users] Java security: mix of unsigned and signed content