[Jmol-users] Jmol single and double quote character

2011-11-24 Thread Martin Hediger
Dear List
What is the syntactic difference in Jmol between single and double quotes?
In Javascript they are interchangeable, but in Jmol not. When is one 
needed and when the other?

Thanks for feedback.

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Re: [Jmol-users] jmol / json / init

2011-11-24 Thread Rolf Huehne
On 11/23/2011 11:11 PM, Tamas Hegedus wrote:
 Rolf,

 The success part is not missing. The callback function is there. The
 data part is missing, I do not send any data to the server, but it seems
 for me that it is not a problem. Javascript recognizes that the second
 'parameter' is the callback function.

My own AJAX experiences (without using any framework) were made a few 
years ago, but as far as I remember the callback function has to deal 
with the different states since it is an asynchronous process in order 
not to block the browser.
My assumption was, that the 'success' keyword in the jQuery API would 
simplify this and the callback function would only have to deal with the 
susccess case (like your function does).  But without that you might 
need to take care of the different states of your request yourself and 
wait until it is finished successfully.
But if you are familiar with the API you will know that better.

Regards,
Rolf

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[Jmol-users] Regarding Visualization problem

2011-11-24 Thread rohit mehrotra
Hi  i am trying to implement the jmol in my application but when i try to
upload the molecule it show's
like FileManager.getAtomSetCollectionFromFile(/media/66881A6A881A394F/1.mol)
FileManager opening /media/66881A6A881A394F/1.mol
openFile(/media/66881A6A881A394F/1.mol): 78 ms
i am unable to visualize my molecule only a blank applets comes kindly
suggest a suitable solution for this problem . And i also want's to know
that can i write the mol2 file using jmol or is there any way to write the
mol2 file using jmol.

-- 
Thanks  Regards
Rohit Mehrotra
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[Jmol-users] MediaWiki Plugin

2011-11-24 Thread Kilian Baerwinkel
Dear all,

I am trying to use Jmol within our Wiki. I have installed the Mediawiki
extension according to the documentation, placing both the source files of
the extension and the files of Jmol in a Jmol folder within the extensions
folder of mediawiki.

Having set
require_once(extensions/Jmol/Jmol.php);
the source code of an applet is no longer displayed, so the parser seems so
acknowledge the presence of known tags,but no applet is displayed.

Did anyone come across this issue, or does anyone see an obvious mistake of
mine?

Many thanks for your help

Kilian Baerwinkel



-- 
__

MSc. Chem. Kilian Bärwinkel

Lehrstuhl für Anorganische Chemie I
Fakultät NW 1
Universität Bayreuth
Universitätsstr. 30
95447 Bayreuth

Tel:+49 921 55 - 4387
Fax:+49 921 55 - 2788

e-mail: kilian.baerwin...@uni-bayreuth.de

http://www.senker.uni-bayreuth.de
--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
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Re: [Jmol-users] MediaWiki Plugin

2011-11-24 Thread Jaime Prilusky
On line 833 of the file Jmol.body.php remove the '' from the third parameter 
of the function jmolTag()

Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot – Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113

OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)

From: Kilian Baerwinkel 
kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de
Reply-To: 
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Thu, 24 Nov 2011 14:15:24 +0100
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: [Jmol-users] MediaWiki Plugin

Dear all,

I am trying to use Jmol within our Wiki. I have installed the Mediawiki 
extension according to the documentation, placing both the source files of the 
extension and the files of Jmol in a Jmol folder within the extensions folder 
of mediawiki.

Having set
require_once(extensions/Jmol/Jmol.php);
the source code of an applet is no longer displayed, so the parser seems so 
acknowledge the presence of known tags,but no applet is displayed.

Did anyone come across this issue, or does anyone see an obvious mistake of 
mine?

Many thanks for your help

Kilian Baerwinkel



--
__

MSc. Chem. Kilian Bärwinkel

Lehrstuhl für Anorganische Chemie I
Fakultät NW 1
Universität Bayreuth
Universitätsstr. 30
95447 Bayreuth

Tel:+49 921 55 - 4387
Fax:+49 921 55 - 2788

e-mail: 
kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de

http://www.senker.uni-bayreuth.de

-- 
All the data continuously generated in your IT infrastructure contains a 
definitive record of customers, application performance, security threats, 
fraudulent activity, and more. Splunk takes this data and makes sense of it. IT 
sense. And common sense. 
http://p.sf.net/sfu/splunk-novd2d___
 Jmol-users mailing list 
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contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
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Re: [Jmol-users] MediaWiki Plugin

2011-11-24 Thread Kilian Baerwinkel
Hello Jaime

Thank you very much for your answer... On line 833, there was no  at the
third parameter, but i fond some more $parser and removed the . This did
not make the applet appear, but now i can see a link if I insert a
jmolfile. Still nothing happens if the link is clicked.

Any ideas?

Best

Kilian

On 24 November 2011 14:34, Jaime Prilusky jaime.prilu...@weizmann.ac.ilwrote:

   On line 833 of the file Jmol.body.php remove the '' from the third
 parameter of the function jmolTag()

  Jaim
 --
Dr Jaime Prilusky
 Head Bioinformatics
 RD Bioinformatics and Data Management
 Department of Biological Services
 Weizmann Institute of Science
 76100 Rehovot – Israel

  mail: jaime.prilu...@weizmann.ac.il
 tel: 972-8-9344959
 fax: 972-8-9344113

  OCA, http://oca.weizmann.ac.il (the protein structure/function database)
 Proteopedia, http://proteopedia.org (because life has more than 2D)

   From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de
 Reply-To: jmol-users@lists.sourceforge.net
 Date: Thu, 24 Nov 2011 14:15:24 +0100
 To: jmol-users@lists.sourceforge.net
 Subject: [Jmol-users] MediaWiki Plugin

  Dear all,

  I am trying to use Jmol within our Wiki. I have installed the Mediawiki
 extension according to the documentation, placing both the source files of
 the extension and the files of Jmol in a Jmol folder within the extensions
 folder of mediawiki.

  Having set
 require_once(extensions/Jmol/Jmol.php);
 the source code of an applet is no longer displayed, so the parser seems
 so acknowledge the presence of known tags,but no applet is displayed.

  Did anyone come across this issue, or does anyone see an obvious mistake
 of mine?

  Many thanks for your help

  Kilian Baerwinkel



  --
 __

  MSc. Chem. Kilian Bärwinkel

  Lehrstuhl für Anorganische Chemie I
 Fakultät NW 1
 Universität Bayreuth
 Universitätsstr. 30
 95447 Bayreuth

  Tel:+49 921 55 - 4387
 Fax:+49 921 55 - 2788

  e-mail: kilian.baerwin...@uni-bayreuth.de

  http://www.senker.uni-bayreuth.de

 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security threats,
 fraudulent activity, and more. Splunk takes this data and makes sense of
 it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d___Jmol-users
  mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users


 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




-- 
__

MSc. Chem. Kilian Bärwinkel

Lehrstuhl für Anorganische Chemie I
Fakultät NW 1
Universität Bayreuth
Universitätsstr. 30
95447 Bayreuth

Tel:+49 921 55 - 4387
Fax:+49 921 55 - 2788

e-mail: kilian.baerwin...@uni-bayreuth.de

http://www.senker.uni-bayreuth.de
--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d___
Jmol-users mailing list
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Re: [Jmol-users] MediaWiki Plugin

2011-11-24 Thread Jaime Prilusky

Take a look to your web server error log file. Sometimes PHP errors appear 
there and you may learn something from that.

Look to the source of the wiki generated page to see if the structure of the 
jmolApplet makes sense.

Create a really simple page with only an applet, no links nor text and try to 
make it work.

Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot – Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113

OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)

From: Kilian Baerwinkel 
kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de
Reply-To: 
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Thu, 24 Nov 2011 15:23:43 +0100
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] MediaWiki Plugin

Hello Jaime

Thank you very much for your answer... On line 833, there was no  at the third 
parameter, but i fond some more $parser and removed the . This did not make 
the applet appear, but now i can see a link if I insert a jmolfile. Still 
nothing happens if the link is clicked.

Any ideas?

Best

Kilian

On 24 November 2011 14:34, Jaime Prilusky 
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
On line 833 of the file Jmol.body.php remove the '' from the third parameter 
of the function jmolTag()

Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot – Israel

mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113

OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)

From: Kilian Baerwinkel 
kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de
Reply-To: 
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Thu, 24 Nov 2011 14:15:24 +0100
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: [Jmol-users] MediaWiki Plugin

Dear all,

I am trying to use Jmol within our Wiki. I have installed the Mediawiki 
extension according to the documentation, placing both the source files of the 
extension and the files of Jmol in a Jmol folder within the extensions folder 
of mediawiki.

Having set
require_once(extensions/Jmol/Jmol.php);
the source code of an applet is no longer displayed, so the parser seems so 
acknowledge the presence of known tags,but no applet is displayed.

Did anyone come across this issue, or does anyone see an obvious mistake of 
mine?

Many thanks for your help

Kilian Baerwinkel



--
__

MSc. Chem. Kilian Bärwinkel

Lehrstuhl für Anorganische Chemie I
Fakultät NW 1
Universität Bayreuth
Universitätsstr. 30
95447 Bayreuth

Tel:+49 921 55 - 4387tel:%2B49%20921%2055%20-%204387
Fax:+49 921 55 - 2788tel:%2B49%20921%2055%20-%202788

e-mail: 
kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de

http://www.senker.uni-bayreuth.de

-- 
All the data continuously generated in your IT infrastructure contains a 
definitive record of customers, application performance, security threats, 
fraudulent activity, and more. Splunk takes this data and makes sense of it. IT 
sense. And common sense. 
http://p.sf.net/sfu/splunk-novd2d___
 Jmol-users mailing list 
Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users

--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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--
__

MSc. Chem. Kilian Bärwinkel

Lehrstuhl für Anorganische Chemie I
Fakultät NW 1
Universität Bayreuth
Universitätsstr. 30
95447 Bayreuth

Tel:+49 921 55 - 4387
Fax:+49 921 55 - 2788

e-mail: 
kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de

http://www.senker.uni-bayreuth.de

-- 
All the data continuously generated in your IT infrastructure contains a 
definitive record of customers, application performance, security 

[Jmol-users] isosurface mep and mo on a plane

2011-11-24 Thread Xavier Prat-Resina
Hi,

I'm trying to represent a MEP on a plane using the charges of a Gaussian
file.
The command I use is:
isosurface color absolute -0.1 0.1 plae xz mep
but nothing gets displayed and the console says:
isosurface created with cutoff=NaN min=0.0 max=0.0; isosurface count:0

However, if I want to represent a MO on a plane using a very similar syntax
it works just fine.
isosurface color absolute -0.1 0.1 plane xz mo 10

Am I missing any keyword?
I have a test page showing my problem
http://chemed.umr.umn.edu/~xavier/modelstest/

Thanks

Xavier

-- 
Xavier Prat-Resina
Assistant Professor
University of Minnesota Rochester.
111 South Broadway, Suite 300
Rochester, Minnesota 55904

Phone: 507-258-8215
E-mail: pratr...@r.umn.edu
http://www.r.umn.edu/faculty/pratr001
--
All the data continuously generated in your IT infrastructure 
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security threats, fraudulent activity, and more. Splunk takes this 
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Re: [Jmol-users] Jmol single and double quote character

2011-11-24 Thread Angel Herráez
Martin,

This is not an authoritative response, but I think it is correct:

Jmol needs double quotes in a few commands, like in loading multiple 
files (filenames between quotes), loading a filename that contains 
problematic characters, load filter, and a few others.

As far as I remember ir never uses single quotes.

So the problem is in writing the javascript; sometimes you must 
change yor quotes in javascript so that the embedded Jmol commands 
can use their double quotes.

Do you have any case where you have found a problem?



--
All the data continuously generated in your IT infrastructure 
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security threats, fraudulent activity, and more. Splunk takes this 
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Re: [Jmol-users] Regarding Visualization problem

2011-11-24 Thread Angel Herráez
Hello Rohit 

1.
I have no experience in embedding Jmol within another applet or app, 
but I ahev experience using the Jmol applet.
Are you aware of the Java security limitations when using the 
unsigned applet? It cannot access any folder for reading files. That 
might be your problem.
http://wiki.jmol.org/index.php/Jmol_Applet#Unsigned_vs._Signed_Applet_
.26_Data_Access

2.
Have you checked the Java Console for errors? Those may describe the 
cause.

3.
I don't think that Jmol can output MOL2 files, only MOL, PDB and XYZ.
http://chemapps.stolaf.edu/jmol/docs/#writemodel

May I ask why do you need mol2?
You could use a converter like OpenBabel.




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Re: [Jmol-users] MediaWiki Plugin

2011-11-24 Thread Angel Herráez
Hello Kilian

First, to be sure, please confirm that you are using the Jmol 
Mediawiki Extension and what version it is.

Also, version of MediaWiki may be of relevance.

You mention a jmolfile tag but that is not included in v.3.3 which 
is the one documented at the Jmol Wiki.
So I guess you are using the newer version at mediawiki.org (I'm not 
familiar with that one)


We are a bit behind on documentation, I see  :-(




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Re: [Jmol-users] MediaWiki Plugin

2011-11-24 Thread Angel Herráez
Hi Jaime

Do you think that is something that needs a permanent bug fix, or is 
it just a per-case solution?

El 24 Nov 2011 a las 13:34, Jaime  Prilusky escribió:
 On line 833 of the file Jmol.body.php remove the '' from the third 
 parameter of the functionjmolTag()


--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
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Re: [Jmol-users] MediaWiki Plugin

2011-11-24 Thread Jaime Prilusky
Dear Angel,

You are completely right in asking first more information on versions,
before suggesting solutions :-)

We are, at this time, testing the latest stable Jmol (12.2.6) with the
latest stable MediaWiki (1.17.0) and found a problem similar to what
Kilian described, so I suggested the fix that worked for us, without
requesting additional details on Kilian configuration.

I have not enough information as to say if this change should be made
permanent, and what will happen if the 'fixed' Jmol extension is run on a
previous MediaWiki version. What's clear is that some research is required.

Best Regards,
Jaim
--
Dr Jaime Prilusky 
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot ­ Israel

mail: jaime.prilu...@weizmann.ac.il
tel: 972-8-9344959
fax: 972-8-9344113

OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)








On 24/11/2011 6:27 PM, Angel Herráez angel.herr...@uah.es wrote:

Hi Jaime

Do you think that is something that needs a permanent bug fix, or is
it just a per-case solution?

El 24 Nov 2011 a las 13:34, Jaime  Prilusky escribió:
 On line 833 of the file Jmol.body.php remove the '' from the third
 parameter of the functionjmolTag()


--

All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
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security threats, fraudulent activity, and more. Splunk takes this 
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Re: [Jmol-users] isosurface mep and mo on a plane

2011-11-24 Thread Jonathan Gutow
Xavier,
is it the typo in the first line?  You have plae instead of plane.  I have 
no experience trying to map MEP onto a plane, so am not sure if it would work 
otherwise.

Jonathan
On Nov 24, 2011, at 10:18 AM, jmol-users-requ...@lists.sourceforge.net wrote:

 isosurface color absolute -0.1 0.1 plae xz mep
 but nothing gets displayed and the console says:
 isosurface created with cutoff=NaN min=0.0 max=0.0; isosurface count:0
 
 However, if I want to represent a MO on a plane using a very similar syntax
 it works just fine.
 isosurface color absolute -0.1 0.1 plane xz mo 10
 
 Am I missing any keyword?
 I have a test page showing my problem
 http://chemed.umr.umn.edu/~xavier/modelstest/
 
 Thanks
 
 Xavier

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

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contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
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Re: [Jmol-users] isosurface mep and mo on a plane

2011-11-24 Thread Xavier Prat-Resina
Thanks Jonathan,
For a moment I thought it would be as simple as my typo.
But the typo is just in my email, in my tests I wrote plane.
Turkey time now :)

Xavier

On Thu, Nov 24, 2011 at 11:08 AM, Jonathan Gutow gu...@uwosh.edu wrote:

 Xavier,
 is it the typo in the first line?  You have plae instead of plane.  I
 have no experience trying to map MEP onto a plane, so am not sure if it
 would work otherwise.

 Jonathan

 On Nov 24, 2011, at 10:18 AM, jmol-users-request@lists.sourceforge.netwrote:

 isosurface color absolute -0.1 0.1 plae xz mep
 but nothing gets displayed and the console says:
 isosurface created with cutoff=NaN min=0.0 max=0.0; isosurface count:0

 However, if I want to represent a MO on a plane using a very similar syntax
 it works just fine.
 isosurface color absolute -0.1 0.1 plane xz mo 10

 Am I missing any keyword?
 I have a test page showing my problem
 http://chemed.umr.umn.edu/~xavier/modelstest/

 Thanks

 Xavier


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



 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
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 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
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-- 
Xavier Prat-Resina
Assistant Professor
University of Minnesota Rochester.
111 South Broadway, Suite 300
Rochester, Minnesota 55904

Phone: 507-258-8215
E-mail: pratr...@r.umn.edu
http://www.r.umn.edu/faculty/pratr001
--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users