Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Rolf Huehne]

On 11/16/2015 08:24 PM, Eric Martz wrote:
> Bob has said that the signed Jmol_s Java applet will NOT be able to
> write files to the local disk.
>
Eric, do you mean the signed Java applet with the "unsigned" privileges 
only (which was the unsigned applet in the past) or with the full 
"signed" privileges?
With full priviliges saving should work.

Have you actually tried yet if it works or not?

Regards,
Rolf
-- 

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Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
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Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Eric Martz]

Dear Rolf and Bob,

I tested it in June and it didn't work.
In this message in June
http://sourceforge.net/p/jmol/mailman/message/34196031/
Bob said

" I don't plan on having capture available for the applet."

But today IT WORKS!!!

Indeed it opens a file save dialog and you can save to the local disk.
Hooray!
I hope this is intentional, not a bug.

Bob, please confirm that this will remain available -- before I spend a 
lot of time developing a user interface in FirstGlance to save an 
animation for Powerpoint.


-Eric

On 11/16/15 2:33 PM, Rolf Huehne wrote:

On 11/16/2015 08:24 PM, Eric Martz wrote:

Bob has said that the signed Jmol_s Java applet will NOT be able to
write files to the local disk.


Eric, do you mean the signed Java applet with the "unsigned" privileges
only (which was the unsigned applet in the past) or with the full
"signed" privileges?
With full priviliges saving should work.

Have you actually tried yet if it works or not?

Regards,
Rolf


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[Jmol-users] Help to put Jmol on server for multi-GIF

[Eric Martz]

I would like to add a feature to FirstGlance in Jmol. While using it 
(always in a web browser), I would like a button that generates a 
rotating multi-GIF of the current molecular view, for inclusion in a 
slide presentation.


In the Jmol application, a one-line command accomplishes that:

   capture “something.gif” spin Y # THANK YOU BOB!

Examples of such animations can be viewed in this Powerpoint:
https://www.dropbox.com/s/ki7wkuj8ojlvb0f/animation-examples-jmol.pptx?dl=0
(/You don't have to login to dropbox. Click "no thanks, continue to 
download"/.)


Bob has said that the signed Jmol_s Java applet will NOT be able to 
write files to the local disk.


Therefore I think the best solution might be to submit the current model 
and Jmol state script to a server, have the server run Jmol application, 
generate the multi-GIF file, and hand it back to the user for download.


1. Is this the best solution?

2. If so, will someone please guide me in how to do this?

Thanks very much, Eric

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org 

 * Top Five 3D MolVis Tools: Top5.MolviZ.Org 
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 * Education: Biochem in 3D at MolviZ.Org 
 * Find Functional Patches in Proteins: ConSurf 
 * Atlas of Macromolecules: Atlas.MolviZ.Org 
 * Interactive Molecules in Architectural Spaces:
   MolecularPlayground.Org 
 * Workshops: Workshops.MolviZ.Org 

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Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Robert Hanson]

  public boolean allowCapture() {
return !isApplet || isSignedApplet;
  }

Eric, I must have misunderstood you -- I meant no capture for JSmol.
​
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Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Eric Martz]

DOUBLE HOORAY!!!

So I will begin coding a user interface to use capture from the applet 
in a browser.


Thanks Bob,
-Eric

On 11/16/15 6:34 PM, Robert Hanson wrote:

  public boolean allowCapture() {
return !isApplet || isSignedApplet;
  }

Eric, I must have misunderstood you -- I meant no capture for JSmol.
​




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Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Robert Hanson]

better warn them how big these files can get.

On Mon, Nov 16, 2015 at 5:52 PM, Eric Martz 
wrote:

> DOUBLE HOORAY!!!
>
> So I will begin coding a user interface to use capture from the applet in
> a browser.
>
> Thanks Bob,
> -Eric
>
>
> On 11/16/15 6:34 PM, Robert Hanson wrote:
>
>   public boolean allowCapture() {
> return !isApplet || isSignedApplet;
>   }
>
> Eric, I must have misunderstood you -- I meant no capture for JSmol.
> ​
>
>
>
>
>
> --
> Presto, an open source distributed SQL query engine for big data, initially
> developed by Facebook, enables you to easily query your data on Hadoop in a
> more interactive manner. Teradata is also now providing full enterprise
> support for Presto. Download a free open source copy now.
> http://pubads.g.doubleclick.net/gampad/clk?id=250295911=/4140
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


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


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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] help with simple function

[Otis Rothenberger]

Eric,

Quick and dirty check: This works in a script entry field:

function s(arg1) {select @{arg1}}; s oxygen; color pink;

Is the problem that whatever is not in quotes? Quotes were required above.

Otis

--
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o...@chemagic.com
http://chemagic.com

 On Jan 26, 2015, at 1:28 PM, Eric Martz ema...@microbio.umass.edu wrote:
 
 I now have 2 aliases that work perfectly! (See definitions at the 
 bottom below)
 
 q # toggles quality (antialiasdisplay)
 h # toggles selectionhalos
 
 I have been unable to come up with the syntax that would define a 
 function so this:
 
 s whatever
 
 would perform this:
 
 select whatever
 
 For example this does nothing (not even an error):
 
 function s(arg1) {select @{arg1}}
 
 s 5
 
 and neither do 3 other variations I've tried.
 
 Thanks!
 
 --
 These work:
 
 function q() {set antialiasDisplay @{!antialiasDisplay}}
 
 function h() {selectionhalos @{!selectionhalos}}
 
 
 
 
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[Jmol-users] help with simple function

[Eric Martz]

I now have 2 aliases that work perfectly! (See definitions at the 
bottom below)

q # toggles quality (antialiasdisplay)
h # toggles selectionhalos

I have been unable to come up with the syntax that would define a 
function so this:

s whatever

would perform this:

select whatever

For example this does nothing (not even an error):

function s(arg1) {select @{arg1}}

s 5

and neither do 3 other variations I've tried.

Thanks!

--
These work:

function q() {set antialiasDisplay @{!antialiasDisplay}}

function h() {selectionhalos @{!selectionhalos}}




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[Jmol-users] help on conversion to Jmol 14/JSmol

[Jakubowski, Henry]

Hi,

I have what I believe is a trivial problem (for everyone but me) on converting 
Jmol 12 files to Jmol 14/JSmol, but as I am more of a cut-and-paste creator of 
Jmol files, I thought I would seek outside help.

I've created about 100 Jmol files 
(http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/list_of_Chime.htm)
 to accompany my web biochemistry book 
(http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html ).

They are all based on Jmol 12.  I just converted one after downloading the 
latest version of Jmol (14.1.3) yesterday.  I modified a template model from 
David Marcey and Molvisions and pasted in button commands from my previous Jmol 
12 verison.  It works well on my PCs using all browsers.

Here is the new file:   
http://employees.csbsju.edu/hjakubowski/Jmol14/Nucleosome/Nucleosome.htm .

Somehow I magically thought it would work on my Nexus Android tablet as well.  
It didn't as the file loads as a Jmol and not a JSmol file.

I would greatly appreciate it if someone could look at the code and suggest 
changes I could make to allow my files to work on any platform (if this is 
possible).  I think the fix is trivial (but again not for me).

Once I get this file working well, I want to use it as a template to convert 
the rest over time.
Thanks for any help.

Henry Jakubowski, Ph.D.
Professor and Chair, Chemistry Department
College St. Benedict/St John's University
241 Ardolf Science Center
37 S. College Ave.
St. Joseph, MN 56374

O:  320.363.5354
F:  320.363.5582
E:  hjakubow...@csbsju.edumailto:hjakubow...@csbsju.edu
W: http://faculty.csbsju.edu/hjakubowski








[Description: HVJsignature]

Henry Jakubowski, Ph.D.
Professor and Chair, Chemistry Department; Head Biochemistry Program College 
St. Benedict/St John's University
241 Ardolf Science Center
37 S. College Ave.
St. Joseph, MN 56374

O:  320.363.5354
F:  320.363.5582
E:  hjakubow...@csbsju.edumailto:hjakubow...@csbsju.edu
W: http://faculty.csbsju.edu/hjakubowski

[CentEmail2]

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Re: [Jmol-users] help on conversion to Jmol 14/JSmol

[Rolf Huehne]

Am 19.12.2013 13:39, schrieb Jakubowski, Henry:
 Hi,

 I have what I believe is a trivial problem (for everyone but me) on
 converting Jmol 12 files to Jmol 14/JSmol, but as I am more of a
 cut-and-paste creator of Jmol files, I thought I would seek outside help.

 I’ve created about 100 Jmol files
 (http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/list_of_Chime.htm)
 to accompany my web biochemistry book
 (http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html
 ).

 They are all based on Jmol 12. I just converted one after downloading
 the latest version of Jmol (14.1.3) yesterday. I modified a template
 model from David Marcey and Molvisions and pasted in button commands
 from my previous Jmol 12 verison. It works well on my PCs using all
 browsers.

 Here is the new
 file:http://employees.csbsju.edu/hjakubowski/Jmol14/Nucleosome/Nucleosome.htm
 .

 Somehow I magically thought it would work on my Nexus Android tablet as
 well. It didn’t as the file loads as a Jmol and not a JSmol file.

 I would greatly appreciate it if someone could look at the code and
 suggest changes I could make to allow my files to work on any platform
 (if this is possible). I think the fix is trivial (but again not for me).

 Once I get this file working well, I want to use it as a template to
 convert the rest over time.

JSmol is working with your example, at least on my Laptop. I could 
activate it sucessfully by adding the corresponding parameter to your 
example URL:
http://employees.csbsju.edu/hjakubowski/Jmol14/Nucleosome/Nucleosome.htm?_USE=HTML5

If this also works on your Android tablet it seems just to be a 
problem of the automatic switch. Maybe the magic behind this switch 
doesn't work well enough yet.
One way to overcome this would be by adding a manual switch between Jmol 
and JSmol.
Another way would be to use JSmol as default. But this will depend for 
example on the number of atoms in the other structures loaded in your 
pages. On my configuration JSmol handles the 13,000 Atoms from the 
nucleosome page fast enough. But I know that in other configurations 
JSmol might be ten times slower, which might be too slow as a default.
Or one could try to improve the automatic switch, for example by adding 
an Android-specific switch. Although there is Java supposed to be 
generally available on Android it is said to need specifically compiled 
Java programs. So the standard Jmol applet should never work on Android 
platforms.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 296, Amtsgericht Jena
Tax Number: 162/141/08228


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Re: [Jmol-users] help on conversion to Jmol 14/JSmol

[Rolf Huehne]

Am 19.12.2013 17:17, schrieb Angel Herráez:
 Note there is no automatic switch. Just not possible to detect Java
 any more.

I just asked a few days ago if the automatic detection of platforms not 
providing Java is still there and Bob replied that it is.

Regards,
Rolf
-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein

VAT No: DE 153 925 464
Register of Associations: No. 296, Amtsgericht Jena
Tax Number: 162/141/08228


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Re: [Jmol-users] help on conversion to Jmol 14/JSmol

[Angel Herráez]

Note there is no automatic switch. Just not possible to detect Java 
any more.

1. The page source may by default activate either Java or HTML5 
formats.
2. If the URL has the special switch, it will override what the page 
source has. (I haven't experimented with this switch yet, implemented 
in Jmol 14)
3. You may add in your page source some javascript that detects e.g. 
the userAgent string and acts accordingly in setting the default 
variant. This I have done in a couple of pages. It is not fully 
foolproof since it relies of the userAgent. You may try to target 
Android and iOS devices.
4. In addition, you can add 2 links or buttons in your page that will 
reload with either option, Java or HTML5, per user choice. In that 
way no one will be cornered into a version that does not work in 
their system. It is also possible without page reload, reinjecting 
the Jmol object code into its container.

Sorry I cannot be more explanative now. Too many things to do before 
the holidays!
Henry, I will be happy to work along with you if you need help on 
this, at some later dates.





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Re: [Jmol-users] Help: trying to create a morph showing open and closed conformations of a dimer. Have 3 models for start (Nikki Hunter)

[Wayne Decatur]

Hi Nikki,
In case you still need more guidance on creating Morphs, another good resource 
is the Proteopedia page on 'Morphs'. See 
http://proteopedia.org/wiki/index.php/Morphs .
Wayne


Message: 4
Date: Tue, 8 Oct 2013 12:44:51 -0400
From: Nikki Hunter nikki.s.hun...@gmail.com
Subject: [Jmol-users] Help: trying to create a morph showing open and
    closed conformations of a dimer. Have 3 models for start
To: Jmol-users@lists.sourceforge.net
Message-ID:
    CAA4RVHmepgTYbmgzNpViK8x6bkOVMZYd0Wcs9pt6u3fGE=e...@mail.gmail.com
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[Jmol-users] Help: trying to create a morph showing open and closed conformations of a dimer. Have 3 models for start

[Nikki Hunter]

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Re: [Jmol-users] Help: trying to create a morph showing open and closed conformations of a dimer. Have 3 models for start

[Robert Hanson]

no message here? But in any case, there was a morph problem with multiple
files; fixed in
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.8_2013.10.08.zip. To do this,
you would use:

load trajectories file1.pdb file2.pdb file3.pdb
animation morph 30
animation on

perhaps


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] Help

[Madhuri Patel]

Hello,

I need some help on how to add another structure in Jmol. I am working with
Tobacco mosaic virus,  have the structure in Jmol and now I want to add the
same structure twice, I am trying to build a structure with multiple
Tobacco mosaic virus structure together. So i jsut need to know how I can
add multiple structures at once in Jmol, that too being the same structure.

-- 
*Sincerely,

Madhuri Patel
SouthUniversity | PharmD Candidate
Class of 2015- Columbia
*
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Re: [Jmol-users] Help

[Angel Herráez]

Hello Madhuri Patel 

Try 

 load files myfile.pdb myfile.pdb

See
http://chemapps.stolaf.edu/jmol/docs/#loadfiles
for more info

PS: try to use a more meaningful phrase in the email subject -- please help 
is not appropriate since it does not allow users to see what the message is 
about, particularly since this goes into the email list archive with thousands 
of 
messages


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[Jmol-users] Help please (Tiqing Liu)

[Liu, Tiqing]

Hi Angel,

  Thank you for your suggestion.  Two snapshots are enclosed for your review.

Please click http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP
Please click 
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSImonomerid=50332929polymerid=p5494seq=100title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34


---
All the best to you,

Tiqing Liu, Ph. D.
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Re: [Jmol-users] Help please (Tiqing Liu)

[Angel Herráez]

Sorry, Tiqing, but I do not see what the problem is. The proteins in those two 
pages
  
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSImonomerid=50332929
polymerid=p5494seq=100title=pound34Thymidylate%20kinasepou
nd34%20AND%20pound34CHEMBL394429pound34

and 
 http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP

look similar to me.
What is the defect you are seeing?

Also, as I said in my former message, select model=1.1 is OK, but  select 
model=3 does not work. You need select 3.0 or select file=3 to select all 
3 models in that file. Maybe that is the origin of the problem.

Try to change to:


  var jmolcmds = [ load http://bdb4.ucsd.edu${hmap.url}.pdb;,
  set appendNew true,
  load APPEND http://bdb4.ucsd.edu${hmap.url}_ligand0.mol2;,
  load APPEND http://bdb4.ucsd.edu${hmap.url}-results.mol2;,
  set frank off,
  model 0,
  select 1.1; spacefill off; cpk off; wireframe off; cartoon; color cartoon 
translucent,
  select 2.1; wireframe 80; spacefill 0.35; center hetero; color translucent; 
zoom 200,
  select 3.0; wireframe off; cpk off; spacefill off,
  background white,
  display all
 ];

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Re: [Jmol-users] Help please (Tiqing Liu)

[Liu, Tiqing]

Hi Angel,

  Thank you for the reply.

  In http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP, the multi layer 
means one protein (as model=1.1), one crystal ligand (as model=2.1), and the 
other ligands (as model=3).

var jmolcmds = [ load http://bdb4.ucsd.edu${hmap.url}.pdb;,
  set appendNew true,
  load APPEND http://bdb4.ucsd.edu${hmap.url}_ligand0.mol2;,
  load APPEND http://bdb4.ucsd.edu${hmap.url}-results.mol2;,
  set frank off,
  model 0,
  select model=1.1; spacefill off; cpk off; wireframe off; 
cartoon; color cartoon translucent; zoom 200,
  select model=2.1; wireframe 80; spacefill 0.35; center 
hetero; color translucent; zoom 200,
  select model=3; wireframe off; cpk off; spacefill off,
  background white,
  display all
];
jmolInitialize(/bind/jmol-13.0.18/,true);
jmolApplet( 600, jmolcmds.join(;), ${pdb} );
jmolBr();

  I agree that single protein behaves nicely at 
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSImonomerid=50332929polymerid=p5494seq=100title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34.
  But did you try http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP.  I 
would like jmol show the protein in 
http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP as protein displayed in 
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSImonomerid=50332929polymerid=p5494seq=100title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34

  Thank you in advance.

PS.  the two are posted again

http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSImonomerid=50332929polymerid=p5494seq=100title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34
http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP

---
All the best to you,

Tiqing Liu, Ph. D.


Message: 1
Date: Thu, 22 Aug 2013 20:22:55 +0200
From: Angel Herr?ez angel.herr...@uah.es
Subject: Re: [Jmol-users] Help please
To: jmol-users@lists.sourceforge.net
Message-ID: 521656ff.6419.f3faf...@angel.herraez.uah.es
Content-Type: text/plain; charset=US-ASCII

Hello Liu

Can you be more specific? That would help.

By multiple layer, do you mean several models (frames) are loaded
together? Or something else?

  http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP does not
behave where not all the atoms and bonds in protein are cartooned.

Which parts of the protein are not displayed? I just loaded the pdb into Jmol
and I see no problem in the cartoon.


Finally, this will not affect, but for your information
you do not need to repeat  set appendNew true,
and zoom applies to all models at the same time, so no need to repeat it.

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[Jmol-users] Help please

[Liu, Tiqing]

Dear Group,

  I am a developer in www.bindingdb.org using Jmol for some displays, like 
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1MRSmonomerid=50132286polymerid=p5494seq=100title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEBI:270373pound34,
 and multiple layers http://bdb4.ucsd.edu/data/surflex/1G6S_S3P/1G6S_S3P.html.

  But a similar multiple layer 
http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP does not behave where 
not all the atoms and bonds in protein are cartooned.  All the multiple layer 
displays are wrote with the same procedures.  A part of javascripts is listed 
in the the following for your review.

var jmolcmds = [ load 
http://bdb4.ucsd.edu/data/surflex/1GSI_TMP/1GSI.pdb;,
  set appendNew true,
  load APPEND 
http://bdb4.ucsd.edu/data/surflex/1GSI_TMP/1GSI_ligand0.mol2;,
  set appendNew true,
  load APPEND 
http://bdb4.ucsd.edu/data/surflex/1GSI_TMP/1GSI-results.mol2;,
  set frank off,
  model 0,
  select model=1.1; spacefill off; cpk off; wireframe off; 
cartoon; color cartoon translucent; zoom 200,
  select model=2.1; wireframe 80; spacefill 0.35; center 
hetero; color translucent; zoom 200,
  select model=3; wireframe off; cpk off; spacefill off,
  background white,
  display all

  The files are could be downloaded through the URLs.

  Thank you in advance for your diagnoses and solution.


---
All the best to you,

Tiqing Liu, Ph. D.
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Re: [Jmol-users] Help please

[Angel Herráez]

Hello Liu

Can you be more specific? That would help.

By multiple layer, do you mean several models (frames) are loaded 
together? Or something else?

  http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSIHET=TMP does not 
behave where not all the atoms and bonds in protein are cartooned. 

Which parts of the protein are not displayed? I just loaded the pdb into Jmol 
and I see no problem in the cartoon.


Finally, this will not affect, but for your information
you do not need to repeat  set appendNew true,
and zoom applies to all models at the same time, so no need to repeat it.



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Re: [Jmol-users] Help please

[Angel Herráez]

Not sure if / how this would affect the protein, but I think instead of using
 select model=3;

you need to use
 select 3.0;
or 
 select file=3;

(those will select all models in the 3rd file, which seems to be your intention 
since file nr.3 has 4 models)



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Re: [Jmol-users] Help With Project Direction

[Angel Herráez]

Hi Aaron 

Thanks for the details. The problem of folding is of my interest.

I'm hesitant to push you back, but certainly I increasingly think this may be 
not reasonable.

 I'm beginning to feel this project may be too ambitious. Is there some other 
 3D visualization tool you know of, which does have such capability? Aside 
 from difficulty, do you feel this is a worthy endeavour? I'm starting to 
 worry that even if I did obtain molecularly 'valid' structures, they would be 
 so different from the folded hp model that most meaning would be lost. 

I don't think it is a question of what visualization tool you use, but of the 
(molecular level) rationale behind the problem.



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Re: [Jmol-users] Help With Project Direction

[Robert Hanson]

I would say this goes far beyond the capability of Jmol. You will need way
more sophisticated tools to do those adjustments


On Thu, Apr 25, 2013 at 7:27 PM, Aaron Germuth germ...@unbc.ca wrote:

  I'm interested in your project and will be happy to collaborate with you.

 Since I'm doing this project through my University, I'm not sure if I'm
 legally allowed to let you help with the physical code portion. I'll have
 to get back to you. However, If this is allowed, I would gladly embrace
 your help.

  what is exactly the HP protein folding model ?

 The HP Protein Folding Model is a simplified model which computers can use
 to fold proteins. Computationally, folding proteins is a very expensive
 process. Even with the massive simplification that there are only two
 different types of amino acids the process still takes an unreasonable
 amount of time for large proteins. And this isn't even considering hydrogen
 bonds or ionic interactions.
 Anyway, in the model, we turn each amino acid into either a hydrophobic or
 hydrophilic amino acid, and allow a genetic algorithm to attempt to put
 hydrophobic amino acids on the inside, and hydrophilic amino acids on the
 outside. The resulting polypeptide is our folded protein.
 This has a little bit more information 
 http://en.wikipedia.org/wiki/Hydrophobic-polar_protein_folding_model;

   the amino acid residues will not necessarily fit in those cells

 This is a problem I've thought about, as some amino acids such as
 phenylalanine are much larger than say, glycine. The goal I'm personally
 going for is to get as close as we can  to the folded model, while obeying
 molecular structure. We might have to edit the Jmol structure if overlap
 occurs.

  a realistic polypeptide backbone will not match the 90 degree angles.

 This goes as before. We can attempt to rotate the peptide bond as much as
 possible to get the closest match.

  it is arguable whether inserting the structure of each amino acid
 residue into it is meaningful.

 The results given from the finished project also are not expected to give
 entirely realistic proteins. However, the results we do obtain can be
 directly compared to an experimentally found .pdb of proteins. This allows
 a direct comparison between computer generated results and the actual
 protein. To evaluate the results of the algorithm before, we simply had to
 observe that hydrophobic residues appeared in the middle, and hydrophilic
 residues on the outside.

 If you have any other questions I'd be happy to answer them.

 Aaron Germuth


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Chair, Chemistry Department
St. Olaf College
Northfield, MN
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Re: [Jmol-users] Help With Project Direction

[Angel Herráez]

More than whteher Jmolis capable or not, my icreasing concern is 
whether this makes sense.

 I would say this goes far beyond the capability of Jmol. You will 
 need way more sophisticated tools to do those adjustments

 Since I'm doing this project through my University, I'm not sure if 
 I'm legally allowed to let you help with the physical code portion. 
 I'll have to get back to you. However, If this is allowed, I would 
 gladly embrace your help.

Well, after all, your email was entitled Help ;-)
I understand.


 The HP Protein Folding Model is a simplified model which computers 
 can use to fold proteins. 

I realize what the basis and limitations are. Is this HP an 
algorithm you have developed, is it published?


 This is a problem I've thought about, as some amino acids such as 
 phenylalanine are much larger than say, glycine. The goal I'm 
 personally going for is to get as close as we can to the folded 
 model, while obeying molecular structure. We might have to edit the 
 Jmol structure if overlap occurs.

Not only overlap, but unrealistic bonding distances. I'm not sure 
this is sensible.


 This goes as before. We can attempt to rotate the peptide bond as 
 much as possible to get the closest match.

You see? Speaking of rotating the bonds as much as possible is scary. 
Peptide bonds do have their prefered orientations.


 The results given from the finished project also are not expected to 
 give entirely realistic proteins. 

Certainly not.

 However, the results we do obtain 
 can be directly compared to an experimentally found .pdb of proteins. 

Not necessarily; too many constraints in the approximation. I'm not 
sure any comparison can be made.


 To evaluate the results of the algorithm 
 before, we simply had to observe that hydrophobic residues appeared 
 in the middle, and hydrophilic residues on the outside.

That you are already seeing with your lattice model. You don't need 
the residues structures.

Anyway, I wish you good luck, but I'd say think it twice before 
embarking into this.

·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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Re: [Jmol-users] Help With Project Direction

[Angel Herráez]

Yes, that's more or less what I understood of how it works.

 The folding model does not deal with anything at the level of
 atoms, only amino acids. 

Yes. So it is arguable whether inserting the structure of each amino 
acid residue into it is meaningful.


 I'm not sure what you mean by minimization. 

minimization refers to the proposed intention of arranging the 
amino acid residue in some reasonabvle orientation for it to bind the 
neighbour residues. Questionable, as I said.




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Re: [Jmol-users] Help With Project Direction

[Aaron Germuth]

 I'm interested in your project and will be happy to collaborate with you.

Since I'm doing this project through my University, I'm not sure if I'm legally 
allowed to let you help with the physical code portion. I'll have to get back 
to you. However, If this is allowed, I would gladly embrace your help.

 what is exactly the HP protein folding model ?

The HP Protein Folding Model is a simplified model which computers can use to 
fold proteins. Computationally, folding proteins is a very expensive process. 
Even with the massive simplification that there are only two different types of 
amino acids the process still takes an unreasonable amount of time for large 
proteins. And this isn't even considering hydrogen bonds or ionic interactions.
Anyway, in the model, we turn each amino acid into either a hydrophobic or 
hydrophilic amino acid, and allow a genetic algorithm to attempt to put 
hydrophobic amino acids on the inside, and hydrophilic amino acids on the 
outside. The resulting polypeptide is our folded protein.
This has a little bit more information 
http://en.wikipedia.org/wiki/Hydrophobic-polar_protein_folding_model;

  the amino acid residues will not necessarily fit in those cells

This is a problem I've thought about, as some amino acids such as phenylalanine 
are much larger than say, glycine. The goal I'm personally going for is to get 
as close as we can  to the folded model, while obeying molecular structure. We 
might have to edit the Jmol structure if overlap occurs.

 a realistic polypeptide backbone will not match the 90 degree angles.

This goes as before. We can attempt to rotate the peptide bond as much as 
possible to get the closest match.

 it is arguable whether inserting the structure of each amino acid residue 
 into it is meaningful.

The results given from the finished project also are not expected to give 
entirely realistic proteins. However, the results we do obtain can be directly 
compared to an experimentally found .pdb of proteins. This allows a direct 
comparison between computer generated results and the actual protein. To 
evaluate the results of the algorithm before, we simply had to observe that 
hydrophobic residues appeared in the middle, and hydrophilic residues on the 
outside.

If you have any other questions I'd be happy to answer them.

Aaron Germuth

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[Jmol-users] Help with Project Direction

[germoose]

Greetings, 

Previously I have created a program which takes a sequence of hydrophobic or
hydrophilic amino acids and folds it based of the HP protein folding model.
The folded coordinates are given and displayed in a x-y-z grid format (as in
an amino acid can only be located on integer x, y, z coordinates; no
decimals). A typical folded protein resembles this:

http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg 

What I hoping to add is to use Jmol to display this protein. However,
instead of simply a ball representing the amino acid, I would like to show
each molecule of each amino acid. 

My current idea of how I would go about this is as such:

- Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this
into a string of hydrophobic or hydrophilic amino acids for my program to
fold. 
- Once folded, replace each amino acid with it's actual molecules in Jmol,
to do this I might
 - programmatically create a .pdb file for Jmol to read. To do this I
would already have pdb files for all 20 amino acids stored, and displace
their atoms to the grid coordinate given from the existing program. However,
I would have to get the amino acids to be bonded together through peptide
bonds, which seems tricky. 

Before I step into this large project, I would just like to ensure I'm on
the right path and doing things the best/easiest way possible. I am quite
new to Jmol and would very much appreciate any suggestions or things to look
out for. If you have any questions, I am more than happy to answer them. 

Thank you for your time 
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[Jmol-users] Help with Project Direction

[germoose]

Greetings, 

Previously I have created a program which takes a sequence of hydrophobic or
hydrophilic amino acids and folds it based of the HP protein folding model.
The folded coordinates are given and displayed in a x-y-z grid format (as in
an amino acid can only be located on integer x, y, z coordinates; no
decimals). A typical folded protein resembles this:

http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg 

What I hoping to add is to use Jmol to display this protein. However,
instead of simply a ball representing the amino acid, I would like to show
each molecule of each amino acid. 

My current idea of how I would go about this is as such:

- Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this
into a string of hydrophobic or hydrophilic amino acids for my program to
fold. 
- Once folded, replace each amino acid with it's actual molecules in Jmol,
to do this I might
 - programmatically create a .pdb file for Jmol to read. To do this I
would already have pdb files for all 20 amino acids stored, and displace
their atoms to the grid coordinate given from the existing program. However,
I would have to get the amino acids to be bonded together through peptide
bonds, which seems tricky. 

Before I step into this large project, I would just like to ensure I'm on
the right path and doing things the best/easiest way possible. I am quite
new to Jmol and would very much appreciate any suggestions or things to look
out for. If you have any questions, I am more than happy to answer them. 

Thank you for your time
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[Jmol-users] Help With Project Direction

[Aaron Germuth]

Greetings,

Previously I have created a program which takes a sequence of hydrophobic or 
hydrophilic amino acids and folds it based of the HP protein folding model. The 
folded coordinates are given and displayed in a x-y-z grid format (as in an 
amino acid can only be located on integer x, y, z coordinates; no decimals). A 
typical folded protein resembles this:

http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg

What I hoping to add is to use Jmol to display this protein. However, instead 
of simply a ball representing the amino acid, I would like to show each 
molecule of each amino acid.

My current idea of how I would go about this is as such:

- Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this into 
a string of hydrophobic or hydrophilic amino acids for my program to fold.
- Once folded, replace each amino acid with it's actual molecules in Jmol, to 
do this I might
 - programmatically create a .pdb file for Jmol to read. To do this I would 
already have pdb files for all 20 amino acids stored, and displace their atoms 
to the grid coordinate given from the existing program. However, I would have 
to get the amino acids to be bonded together through peptide bonds, which seems 
tricky.

Before I step into this large project, I would just like to ensure I'm on the 
right path and doing things the best/easiest way possible. I am quite new to 
Jmol and would very much appreciate any suggestions or things to look out for. 
If you have any questions, I am more than happy to answer them.

Thank you for your time

Aaron

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Re: [Jmol-users] Help with Project Direction

[Robert Hanson]

This sounds very interesting. When you do the folding, do you do it
strictly in terms of residue locations in space? That is, no real atoms? Or
is there at least a backbone to work with?


On Wed, Apr 24, 2013 at 1:54 AM, germoose germ...@unbc.ca wrote:


 Greetings,

 Previously I have created a program which takes a sequence of hydrophobic
 or
 hydrophilic amino acids and folds it based of the HP protein folding model.
 The folded coordinates are given and displayed in a x-y-z grid format (as
 in
 an amino acid can only be located on integer x, y, z coordinates; no
 decimals). A typical folded protein resembles this:

 http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
 http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
 http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg

 What I hoping to add is to use Jmol to display this protein. However,
 instead of simply a ball representing the amino acid, I would like to show
 each molecule of each amino acid.

 My current idea of how I would go about this is as such:

 - Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this
 into a string of hydrophobic or hydrophilic amino acids for my program to
 fold.
 - Once folded, replace each amino acid with it's actual molecules in Jmol,
 to do this I might
  - programmatically create a .pdb file for Jmol to read. To do this I
 would already have pdb files for all 20 amino acids stored, and displace
 their atoms to the grid coordinate given from the existing program.
 However,
 I would have to get the amino acids to be bonded together through peptide
 bonds, which seems tricky.

 Before I step into this large project, I would just like to ensure I'm on
 the right path and doing things the best/easiest way possible. I am quite
 new to Jmol and would very much appreciate any suggestions or things to
 look
 out for. If you have any questions, I am more than happy to answer them.

 Thank you for your time
 --
 View this message in context:
 http://old.nabble.com/Help-with-Project-Direction-tp35329120p35329120.html
 Sent from the jmol-users mailing list archive at Nabble.com.



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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Help with Project Direction

[Robert Hanson]

It seems to me there will be a significant amount of minimization to be
done. That is beyond the scope of Jmol. Jmol can minimize small sections of
a model, but not a full protein.


On Wed, Apr 24, 2013 at 9:27 AM, Robert Hanson hans...@stolaf.edu wrote:

 This sounds very interesting. When you do the folding, do you do it
 strictly in terms of residue locations in space? That is, no real atoms? Or
 is there at least a backbone to work with?


 On Wed, Apr 24, 2013 at 1:54 AM, germoose germ...@unbc.ca wrote:


 Greetings,

 Previously I have created a program which takes a sequence of hydrophobic
 or
 hydrophilic amino acids and folds it based of the HP protein folding
 model.
 The folded coordinates are given and displayed in a x-y-z grid format (as
 in
 an amino acid can only be located on integer x, y, z coordinates; no
 decimals). A typical folded protein resembles this:

 http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
 http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
 http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg

 What I hoping to add is to use Jmol to display this protein. However,
 instead of simply a ball representing the amino acid, I would like to show
 each molecule of each amino acid.

 My current idea of how I would go about this is as such:

 - Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this
 into a string of hydrophobic or hydrophilic amino acids for my program to
 fold.
 - Once folded, replace each amino acid with it's actual molecules in Jmol,
 to do this I might
  - programmatically create a .pdb file for Jmol to read. To do this I
 would already have pdb files for all 20 amino acids stored, and displace
 their atoms to the grid coordinate given from the existing program.
 However,
 I would have to get the amino acids to be bonded together through peptide
 bonds, which seems tricky.

 Before I step into this large project, I would just like to ensure I'm on
 the right path and doing things the best/easiest way possible. I am quite
 new to Jmol and would very much appreciate any suggestions or things to
 look
 out for. If you have any questions, I am more than happy to answer them.

 Thank you for your time
 --
 View this message in context:
 http://old.nabble.com/Help-with-Project-Direction-tp35329120p35329120.html
 Sent from the jmol-users mailing list archive at Nabble.com.



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 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


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

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




-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Help with Project Direction

[Angel Herráez]

Hello Aaron

I'm interested in your project and will be happy to collaborate with you.

Question: what is exactly the HP protein folding model ?

Comment: apart from the minimization problem that Bob mentions, the issue 
is that given the reticular positions, the amino acid residues will not 
necessarily fit in those cells. It is not just the problem of rotating them 
so 
that they may be bound, but that the size of each residue will not match the 
size of a single cell in the XYZ net. An also, a realistic polypeptide backbone 
will not match the 90 degree angles.
How do you envisage that?




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Re: [Jmol-users] Help With Project Direction

[Aaron Germuth]

The user enters in a sequence of h's and p's, which starts off as a linear 
chain of amino acids. After folding, the linear chain usually takes on a 
'globular' form. Each amino acid is represented as a single red (hydrophobic) 
or blue (hydrophilic) sphere. The folding model does not deal with anything at 
the level of atoms, only amino acids. I hope this answers your question.

Aaron Germuth

This sounds very interesting. When you do the folding, do you do it
strictly in terms of residue locations in space? That is, no real atoms? Or
is there at least a backbone to work with?


I'm not sure what you mean by minimization. Keep in mind this program is just 
an educational model and is not meant for proteins thousands of amino acids 
long. In fact, attempting to fold a protein even one hundred amino acids long 
would take over a day. I intend to use this only on very small proteins. 

Aaron Germuth
-
It seems to me there will be a significant amount of minimization to be
done. That is beyond the scope of Jmol. Jmol can minimize small sections of
a model, but not a full protein.

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Re: [Jmol-users] help - Question about JSmol

[Jonathan Gough]

Bob,

I'm still having a hard time figuring this out.

1 - I believe that the following page is picking up everything from you
page, and the right click menu isn't working.  Would the problem be with
out server or am I still missing something?
http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm

2- RE: corrupted files.  What I did previously was, download (via chrome)
unzip (via my mac's default application) the jsmol folder was moved to the
website directory (in a dropbox folder elsewhere on my mac) and then
uploaded to the server via the ftp protocol built into dreamweaver 5.5.
That failed so I tried this - used wget to download the file on a linux box
(centOS 5).  used bash unzip, scp to the website directory on my mac, then
ftp via dreamweaver.  That also failed (and is what is up now).

In theory I could ftp straight from the linux box, but I can't figure out
exactly how to do that.  Can you advise on how I might proceed?

Thanks,
Jonathan



On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough
jonathan.d.go...@gmail.comwrote:

 Thanks for getting back to me Bob,

 I am using a mac, but I didn't edit those files.   In fact, I
 re-downloaded everything and the problem is the same.  I even used wget
 from a linux box to grab the files from your machine and they are
 identical.  if you go to
 http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
 source, there isn't any gaps.  I used vi, and couldn't see any gaps either.

 if for some reason they are there, how would I go about getting rid of
 them?  any other ideas?

 thanks,
 Jonathan


 On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan



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Re: [Jmol-users] help - Question about JSmol

[Angel Herráez]

Hi Jonathan

I don't think that download or ftp will be your problem. It is a 
zipfile, so the contents will not be altered during file retrieval.
Make sure you are downloading the correct file,
http://chemapps.stolaf.edu/jmol/jsmol.zip

Then it might be a question of how it is unzipped, but I would not 
expect so. As long as you don't edit the files contained in the zip, 
they should be preserved as they were.

(I run Windows, so I cannot really assess exactly the different 
behaviour of CR vs CRLF in the files.)
I have been using the downloaded jsmol.zip without trouble.



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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

On Fri, Jan 25, 2013 at 5:28 PM, Jonathan Gough
jonathan.d.go...@gmail.comwrote:

 Bob,

 I'm still having a hard time figuring this out.


sounds very frustrating. I am 100% sure it is a tool you are using
somewhere along the line, but not being very adept with Macs, I can't
really give you much of a hand. Perhaps a user more familiar with Macs can
suggest a binary file reader -- something that opens files on a Mac and
allows you to look at the binary code. You are looking for 0D 0D 0A.
Whatever program is creating that, that's your problem. You could also go
by file size. The corrupted files are much longer than the correct ones.



 1 - I believe that the following page is picking up everything from you
 page, and the right click menu isn't working.  Would the problem be with
 out server or am I still missing something?
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm


OK, here is what is unusual:

j2sPath: http://chemapps.stolaf.edu/jmol/jsmol/j2s;


So your idea is to load all the JavaScript from St. Olaf. It certainly
MIGHT work. By the way, you can replace all those .js sources by


script type=text/javascript
src=http://chemapps.stolaf.edu/jmol/jsmol/
view-source:http://chemapps.stolaf.edu/jmol/jsmol/JSmoljQuery.jsJSmol.min.js/script

But, the general problem here is that you probably should not link to
chemapps.stolaf.edu that way. I change those files routinely, and my
uploads will likely break your pages while they are happening.

Still, I don't see why exactly it happens only when the menu is loaded.
Very odd!

Bob



 2- RE: corrupted files.  What I did previously was, download (via chrome)
 unzip (via my mac's default application) the jsmol folder was moved to the
 website directory (in a dropbox folder elsewhere on my mac) and then
 uploaded to the server via the ftp protocol built into dreamweaver 5.5.
 That failed so I tried this - used wget to download the file on a linux
 box (centOS 5).  used bash unzip, scp to the website directory on my mac,
 then ftp via dreamweaver.  That also failed (and is what is up now).

 In theory I could ftp straight from the linux box, but I can't figure out
 exactly how to do that.  Can you advise on how I might proceed?

 Thanks,
 Jonathan



 On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Thanks for getting back to me Bob,

 I am using a mac, but I didn't edit those files.   In fact, I
 re-downloaded everything and the problem is the same.  I even used wget
 from a linux box to grab the files from your machine and they are
 identical.  if you go to
 http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
 source, there isn't any gaps.  I used vi, and couldn't see any gaps either.

 if for some reason they are there, how would I go about getting rid of
 them?  any other ideas?

 thanks,
 Jonathan


 On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan





 --
 Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
 MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
 with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
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-- 
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Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

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

Re: [Jmol-users] help - Question about JSmol

[Jonathan Gough]

At the moment, I am using the St. Olaf packages to trouble shoot the
issues.  If I can't load a simple page that utilizes your code - then in my
mind there is an issue with the server I am using to host the single page,
yes?

I have edited the test page again, simplified the header (I think) and
removed the full path to j2s.  Now it's broken again.  I know it's not the
header, as when I changed that, it still functioned the same.  therefore
there is some issue with the j2s statement.

http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm


On Fri, Jan 25, 2013 at 10:28 AM, Jonathan Gough jonathan.d.go...@gmail.com
 wrote:

 Bob,

 I'm still having a hard time figuring this out.

 1 - I believe that the following page is picking up everything from you
 page, and the right click menu isn't working.  Would the problem be with
 out server or am I still missing something?
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm

 2- RE: corrupted files.  What I did previously was, download (via chrome)
 unzip (via my mac's default application) the jsmol folder was moved to the
 website directory (in a dropbox folder elsewhere on my mac) and then
 uploaded to the server via the ftp protocol built into dreamweaver 5.5.
 That failed so I tried this - used wget to download the file on a linux
 box (centOS 5).  used bash unzip, scp to the website directory on my mac,
 then ftp via dreamweaver.  That also failed (and is what is up now).

 In theory I could ftp straight from the linux box, but I can't figure out
 exactly how to do that.  Can you advise on how I might proceed?

 Thanks,
 Jonathan



 On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Thanks for getting back to me Bob,

 I am using a mac, but I didn't edit those files.   In fact, I
 re-downloaded everything and the problem is the same.  I even used wget
 from a linux box to grab the files from your machine and they are
 identical.  if you go to
 http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
 source, there isn't any gaps.  I used vi, and couldn't see any gaps either.

 if for some reason they are there, how would I go about getting rid of
 them?  any other ideas?

 thanks,
 Jonathan


 On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan




--
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Re: [Jmol-users] help - Question about JSmol

[Jaime Prilusky]

On Jan 25, 2013, at 9:00 PM, Jonathan Gough wrote:

At the moment, I am using the St. Olaf packages to trouble shoot the issues.  
If I can't load a simple page that utilizes your code - then in my mind there 
is an issue with the server I am using to host the single page, yes?

'loadScript' is unable to find the directory 'core' required for the file 
'package.js'
Declaring the path leading to the required directories is needed.

Jaim
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Re: [Jmol-users] help - Question about JSmol

[Angel Herráez]

 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm

I am not sure, but it is possible that this line within Info in your page

j2sPath: j2s,

is read as find the files in subfolder j2s of the current (i.e. this page) 
folder
So it's no surprise that it does not load


I think you sopuld put the whole set of JSmol files in your server. Loading 
page and code from a mixture of servers is harder to predict.
I can say that when I first tried to use JSmol and pointed to StOlaf server for 
all the javascript, I could not make it work.



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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

What happens when you

1) just download http://chemapps.stolaf.edu/jmol//jsmol.zip, unzip it, and
run jsmol.htm there on your machine. It works, right? With a menu?
2) now upload that directory to a website and try it there. Works or not? I
would think so.
3) now adapt jsmol.htm to your needs or substitute your page and see if
that works.

I think the standard development procedure is basically that -- and, if
desired, then removing directories and/or files that are unnecessary. (You
can find out what is required that is not in the core directory by
inspecting the info panel behind the viewer. using browser developer
tools -- javascript console -- jmolApplet0._showInfo(true)





On Fri, Jan 25, 2013 at 9:00 PM, Jonathan Gough
jonathan.d.go...@gmail.comwrote:

 At the moment, I am using the St. Olaf packages to trouble shoot the
 issues.  If I can't load a simple page that utilizes your code - then in my
 mind there is an issue with the server I am using to host the single page,
 yes?

 I have edited the test page again, simplified the header (I think) and
 removed the full path to j2s.  Now it's broken again.  I know it's not the
 header, as when I changed that, it still functioned the same.  therefore
 there is some issue with the j2s statement.

 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm


 On Fri, Jan 25, 2013 at 10:28 AM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Bob,

 I'm still having a hard time figuring this out.

 1 - I believe that the following page is picking up everything from you
 page, and the right click menu isn't working.  Would the problem be with
 out server or am I still missing something?
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm

 2- RE: corrupted files.  What I did previously was, download (via chrome)
 unzip (via my mac's default application) the jsmol folder was moved to the
 website directory (in a dropbox folder elsewhere on my mac) and then
 uploaded to the server via the ftp protocol built into dreamweaver 5.5.
 That failed so I tried this - used wget to download the file on a linux
 box (centOS 5).  used bash unzip, scp to the website directory on my mac,
 then ftp via dreamweaver.  That also failed (and is what is up now).

 In theory I could ftp straight from the linux box, but I can't figure out
 exactly how to do that.  Can you advise on how I might proceed?

 Thanks,
 Jonathan



 On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Thanks for getting back to me Bob,

 I am using a mac, but I didn't edit those files.   In fact, I
 re-downloaded everything and the problem is the same.  I even used wget
 from a linux box to grab the files from your machine and they are
 identical.  if you go to
 http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
 source, there isn't any gaps.  I used vi, and couldn't see any gaps either.

 if for some reason they are there, how would I go about getting rid of
 them?  any other ideas?

 thanks,
 Jonathan


 On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough 
 jonathan.d.go...@gmail.com wrote:

 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan






 --
 Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
 MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
 with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
 MVPs and experts. ON SALE this month only -- learn more at:
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 ___
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 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




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


If nature does not answer first 

[Jmol-users] help - Question about JSmol

[Jonathan Gough]

Firstly I would like to thank everyone for their hard work on JSmol and
Jmol; Incredible, I love it!

I am working on a website to help students here at LIU who are taking
organic chemistry.

I believe I have figured out how to implement JSmol.  In my testing
however, I have only been able to get JSmol.min.js to work.
For whatever reason, the other, or full packages (JSmoljQuery.js,
JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
page works, but test2.htm does not.

the test pages on my site are here

this works:
http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

this doesn't:
http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

simple-example that works:
http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

simple-example that doesn't work (missing the JSmol.min.js):
http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


I was wondering if anyone could provide some insight.

Sincerely,
Jonathan
--
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

Thank you -- glad you find it useful.

When you copied the files, whatever program you used inadvertently added
extra linefeeds between the lines. So You got:

 'div id=__jsmolformdiv__ style=display:none\

form id=__jsmolform__ method=post 
target=_blank action=\

input name=call value=saveFile/\



instead of

 'div id=__jsmolformdiv__ style=display:none\
form id=__jsmolform__ method=post 
target=_blank action=\
input name=call value=saveFile/\



and that failed. My guess is that you edited that with some tool that
wasn't properly recognizing the two-character CR-LF sequence as a new
line. Perhaps on a Mac? Would TextEdit do that? So it turned those into
CR-CR-LF for some reason, and that broke the code.

Bob Hanson





On Wed, Jan 23, 2013 at 12:02 PM, Jonathan Gough jonathan.d.go...@gmail.com
 wrote:

 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan


 --
 Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
 MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
 with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
 MVPs and experts. ON SALE this month only -- learn more at:
 http://p.sf.net/sfu/learnnow-d2d
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
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Re: [Jmol-users] help - Question about JSmol

[Jonathan Gough]

Thanks for getting back to me Bob,

I am using a mac, but I didn't edit those files.   In fact, I re-downloaded
everything and the problem is the same.  I even used wget from a linux box
to grab the files from your machine and they are identical.  if you go to
http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
source, there isn't any gaps.  I used vi, and couldn't see any gaps either.

if for some reason they are there, how would I go about getting rid of
them?  any other ideas?

thanks,
Jonathan


On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough
jonathan.d.go...@gmail.comwrote:

 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan

--
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. ON SALE this month only -- learn more at:
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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

On Wed, Jan 23, 2013 at 4:09 PM, Jonathan Gough
jonathan.d.go...@gmail.comwrote:

 Thanks for getting back to me Bob,

 I am using a mac, but I didn't edit those files.   In fact, I
 re-downloaded everything and the problem is the same.  I even used wget
 from a linux box to grab the files from your machine and they are
 identical.  if you go to
 http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
 source, there isn't any gaps.  I used vi, and couldn't see any gaps either.



That's because those editors were programmed to ignore this sort of
cross-platform problem. Use a binary file reader. You will see. They are
there. Something you did mangled the files. Mine have

%0D%0A

(CR LF)

yours have

%0D%0D%0A

(CR CR LF)

What I did was to view source at the link you sent me, and then I
right-clicked the link to JSmolCore.js and saved that, then looked at it
with a binary file reader I have.

Mine:

008457:   _jsmolfo
008465:   rmdiv__
008473: 20   style=
008481:   display:
008489:   none\  0D
008497: 0A 09 09 09 09   fo
008505:   rm  20   id=

Yours:

008643:   _jsmolfo
008651:   rmdiv__
008659: 20   style=
008667:   display:
008675:   none\  0D
008683: 0D 0A 09 09 09 09   f
008691:   orm  20   id=

But even just with my browser at your link, above, I see the double
spacing line breaks.



Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. ON SALE this month only -- learn more at:
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Jmol-users mailing list
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[Jmol-users] Help with ChemDoodle Web

[Otis Rothenberger]

All,

I know this is not a ChemDoodle list, but with all the recent ChemDoodle 
activity on the list, I've been playing with the Web Components.

Here's a big frustration, and maybe someone on the list can help me: If I 
literally define a JavaScript molfile variable - e.g.:

lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 
0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 
-0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 
0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 
H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 
1 0 0 0 0\nM END\n\n'

then I can dynamically load it into a Transformer3D Canvas - no problem.

If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of 
the same load routine throws an obscure JS error - TypeError: h is undefined.

If I directly copy the returned AJAX text and paste it into a direct definition 
of lsdfStr, the dynamic load works.

Any thoughts would be appreciated.

Otis

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




--
Better than sec? Nothing is better than sec when it comes to
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Re: [Jmol-users] Help with ChemDoodle Web

[Robert Hanson]

Otis, forget that. Don't go there. Period. This is just what we are setting
up now, and you are going to love it.

1) Use JmolCD.js

2) Follow the lead shown in
http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js
to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose
automatically based on the browser capability.

3) There is no need to have the MOL data stuffed into a variable that way.
Just load the file from your server just like for Jmol, even if it is just
a ChemDoodle canvas, using:

applet.loadFile()


Bob

On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.comwrote:

 All,

 I know this is not a ChemDoodle list, but with all the recent ChemDoodle
 activity on the list, I've been playing with the Web Components.

 Here's a big frustration, and maybe someone on the list can help me: If I
 literally define a JavaScript molfile variable - e.g.:

 lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0
 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.
 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0
 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900
 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n
 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n'

 then I can dynamically load it into a Transformer3D Canvas - no problem.

 If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use
 of the same load routine throws an obscure JS error - TypeError: h is
 undefined.

 If I directly copy the returned AJAX text and paste it into a direct
 definition of lsdfStr, the dynamic load works.

 Any thoughts would be appreciated.

 Otis

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






 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
 http://p.sf.net/sfu/Boundary-dev2dev
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
http://p.sf.net/sfu/Boundary-dev2dev___
Jmol-users mailing list
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Re: [Jmol-users] Help with ChemDoodle Web

[Robert Hanson]

...of course, this is in daily flux, and one thing I haven't implemented is
the fact that you can go directly to resolver now by AJAX. I'm hoping to
get that set up for RCSB as well, and then we will have full resolver/pdb
loading by the UNSIGNED applet. Yeah!

On Wed, Apr 18, 2012 at 9:52 AM, Robert Hanson hans...@stolaf.edu wrote:

 Otis, forget that. Don't go there. Period. This is just what we are
 setting up now, and you are going to love it.

 1) Use JmolCD.js

 2) Follow the lead shown in
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use
 JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have
 Jmol choose automatically based on the browser capability.

 3) There is no need to have the MOL data stuffed into a variable that way.
 Just load the file from your server just like for Jmol, even if it is just
 a ChemDoodle canvas, using:

 applet.loadFile()


 Bob

 On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger 
 osrot...@chemagic.comwrote:

 All,

 I know this is not a ChemDoodle list, but with all the recent ChemDoodle
 activity on the list, I've been playing with the Web Components.

 Here's a big frustration, and maybe someone on the list can help me: If I
 literally define a JavaScript molfile variable - e.g.:

 lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0
 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.
 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0
 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900
 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n
 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n'

 then I can dynamically load it into a Transformer3D Canvas - no problem.

 If on the other hand I define lsdfStr via AJAX to Resolver, subsequent
 use of the same load routine throws an obscure JS error - TypeError: h is
 undefined.

 If I directly copy the returned AJAX text and paste it into a direct
 definition of lsdfStr, the dynamic load works.

 Any thoughts would be appreciated.

 Otis

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






 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
 http://p.sf.net/sfu/Boundary-dev2dev
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




 --
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 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




-- 
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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
http://p.sf.net/sfu/Boundary-dev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Help with ChemDoodle Web

[Kevin Theisen]

Hi Otis,

See if you encounter the same issue with Bob's js script, if you do I will look 
into it. Sometimes AJAX messes with the file line delimiters which can cause 
this issue. I would like to know what exactly is causing this issue though. We 
also just added a new ChemDoodle.io.file.content() function which uses AJAX to 
retrieve file content from a local url. I haven't encountered any issues with 
it yet. More on it is now in the tutorial (in Obtain File Content via AJAX):  
http://web.chemdoodle.com/tutorial/loading-data

Hope this helps,
Kevin



On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote:

 Otis, forget that. Don't go there. Period. This is just what we are setting 
 up now, and you are going to love it.
 
 1) Use JmolCD.js
 
 2) Follow the lead shown in 
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js 
 to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose 
 automatically based on the browser capability. 
 
 3) There is no need to have the MOL data stuffed into a variable that way. 
 Just load the file from your server just like for Jmol, even if it is just a 
 ChemDoodle canvas, using:
 
 applet.loadFile()
 
 
 Bob
 
 On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.com 
 wrote:
 All,
 
 I know this is not a ChemDoodle list, but with all the recent ChemDoodle 
 activity on the list, I've been playing with the Web Components.
 
 Here's a big frustration, and maybe someone on the list can help me: If I 
 literally define a JavaScript molfile variable - e.g.:
 
 lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 
 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 
 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 
 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 
 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 
 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n'
 
 then I can dynamically load it into a Transformer3D Canvas - no problem.
 
 If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of 
 the same load routine throws an obscure JS error - TypeError: h is undefined.
 
 If I directly copy the returned AJAX text and paste it into a direct 
 definition of lsdfStr, the dynamic load works.
 
 Any thoughts would be appreciated.
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 
 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
 http://p.sf.net/sfu/Boundary-dev2dev
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users
 
 
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 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] Help with ChemDoodle Web

[Otis Rothenberger]

Thanks Bob,

That sounds like a plan if I can make it work in our AKA application. On a 3D 
view link in this application, I'm just trying to branch mobile devices to a 
non-Java option. Am I correct in assuming that in:

applet.loadFile()

xxx can be a call to a server side script (my server) that loads a Resolver (or 
PubChem/ChemSpider) SDF file?

Otis



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




On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote:

 Otis, forget that. Don't go there. Period. This is just what we are setting 
 up now, and you are going to love it.
 
 1) Use JmolCD.js
 
 2) Follow the lead shown in 
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js 
 to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose 
 automatically based on the browser capability. 
 
 3) There is no need to have the MOL data stuffed into a variable that way. 
 Just load the file from your server just like for Jmol, even if it is just a 
 ChemDoodle canvas, using:
 
 applet.loadFile()
 
 
 Bob
 
 On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.com 
 wrote:
 All,
 
 I know this is not a ChemDoodle list, but with all the recent ChemDoodle 
 activity on the list, I've been playing with the Web Components.
 
 Here's a big frustration, and maybe someone on the list can help me: If I 
 literally define a JavaScript molfile variable - e.g.:
 
 lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 
 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 
 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 
 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 
 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 
 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n'
 
 then I can dynamically load it into a Transformer3D Canvas - no problem.
 
 If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of 
 the same load routine throws an obscure JS error - TypeError: h is undefined.
 
 If I directly copy the returned AJAX text and paste it into a direct 
 definition of lsdfStr, the dynamic load works.
 
 Any thoughts would be appreciated.
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 
 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
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 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users
 
 
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 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
 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second 
 resolution app monitoring today. Free.
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 https://lists.sourceforge.net/lists/listinfo/jmol-users

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Re: [Jmol-users] Help with ChemDoodle Web

[Robert Hanson]

yeah, yeah. That is PRECISELY what JmolCD.js does. Automatic branching.

On Wed, Apr 18, 2012 at 10:09 AM, Otis Rothenberger
osrot...@chemagic.comwrote:

 Thanks Bob,

 That sounds like a plan if I can make it work in our AKA application. On a
 3D view link in this application, I'm just trying to branch mobile devices
 to a non-Java option. Am I correct in assuming that in:

 applet.loadFile()

 xxx can be a call to a server side script (my server) that loads a
 Resolver (or PubChem/ChemSpider) SDF file?

 Otis



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




 On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote:

 Otis, forget that. Don't go there. Period. This is just what we are
 setting up now, and you are going to love it.

 1) Use JmolCD.js

 2) Follow the lead shown in
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use
 JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have
 Jmol choose automatically based on the browser capability.

 3) There is no need to have the MOL data stuffed into a variable that way.
 Just load the file from your server just like for Jmol, even if it is just
 a ChemDoodle canvas, using:

 applet.loadFile()


 Bob

 On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger 
 osrot...@chemagic.comwrote:

 All,

 I know this is not a ChemDoodle list, but with all the recent ChemDoodle
 activity on the list, I've been playing with the Web Components.

 Here's a big frustration, and maybe someone on the list can help me: If I
 literally define a JavaScript molfile variable - e.g.:

 lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0
 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.
 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0
 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900
 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n
 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n'

 then I can dynamically load it into a Transformer3D Canvas - no problem.

 If on the other hand I define lsdfStr via AJAX to Resolver, subsequent
 use of the same load routine throws an obscure JS error - TypeError: h is
 undefined.

 If I directly copy the returned AJAX text and paste it into a direct
 definition of lsdfStr, the dynamic load works.

 Any thoughts would be appreciated.

 Otis

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






 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
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 --
 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

 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.

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 https://lists.sourceforge.net/lists/listinfo/jmol-users




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-- 
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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
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Re: [Jmol-users] Help with ChemDoodle Web

[Robert Hanson]

On Wed, Apr 18, 2012 at 10:21 AM, Robert Hanson hans...@stolaf.edu wrote:

 yeah, yeah. That is PRECISELY what JmolCD.js does. Automatic branching.

 On Wed, Apr 18, 2012 at 10:09 AM, Otis Rothenberger osrot...@chemagic.com
  wrote:

 Thanks Bob,

 That sounds like a plan if I can make it work in our AKA application. On
 a 3D view link in this application, I'm just trying to branch mobile
 devices to a non-Java option. Am I correct in assuming that in:

 applet.loadFile()

 xxx can be a call to a server side script (my server) that loads a
 Resolver (or PubChem/ChemSpider) SDF file?


For the resolver, just use:

Jmol.searchQuery(applet, $tylenol);

or

applet.setSearchTerm($tylenol);

like that. (These are equivalent)

  $ means NCI; = means PDB:

Jmol.searchQuery(applet, =1dcc);


Bob


 Otis



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




 On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote:

 Otis, forget that. Don't go there. Period. This is just what we are
 setting up now, and you are going to love it.

 1) Use JmolCD.js

 2) Follow the lead shown in
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use
 JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have
 Jmol choose automatically based on the browser capability.

 3) There is no need to have the MOL data stuffed into a variable that
 way. Just load the file from your server just like for Jmol, even if it is
 just a ChemDoodle canvas, using:

 applet.loadFile()


 Bob

 On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.com
  wrote:

 All,

 I know this is not a ChemDoodle list, but with all the recent ChemDoodle
 activity on the list, I've been playing with the Web Components.

 Here's a big frustration, and maybe someone on the list can help me: If
 I literally define a JavaScript molfile variable - e.g.:

 lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0
 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n
 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H
 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0
 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1
 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n'

 then I can dynamically load it into a Transformer3D Canvas - no problem.

 If on the other hand I define lsdfStr via AJAX to Resolver, subsequent
 use of the same load routine throws an obscure JS error - TypeError: h is
 undefined.

 If I directly copy the returned AJAX text and paste it into a direct
 definition of lsdfStr, the dynamic load works.

 Any thoughts would be appreciated.

 Otis

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






 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
 http://p.sf.net/sfu/Boundary-dev2dev
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




 --
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 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

 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.

 http://p.sf.net/sfu/Boundary-dev2dev___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




 --
 Better than sec? Nothing is better than sec when it comes to
 monitoring Big Data applications. Try Boundary one-second
 resolution app monitoring today. Free.
 http://p.sf.net/sfu/Boundary-dev2dev
 ___
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 https://lists.sourceforge.net/lists/listinfo/jmol-users




 --
 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




-- 
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 

[Jmol-users] Help with Firefox 4

[Patrick J. Carroll]

Just installed Firefox 4 on Windows 7 system. Now Java doesn't work!

There was a message during installation that the Java plug-in is incompatible
with Firefox 4. So what do I do?


Pat


Patrick J. Carroll, Ph.D.
Director, X-ray Crystallography Facility
Department of Chemistry
University of Pennsylvania
Philadelphia, PA

Phone: 215-898-3505
Web: http://macxray.chem.upenn.edu

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Re: [Jmol-users] Help with Firefox 4

[Otis Rothenberger]

Pat,

I don't know if I can help you, but I'm sure interested in your problem.

For quite some time now, I have been refusing Java updates on my Window 7 
computer. The reason for this is that every Java update since 1.6.0_21 has 
a security feature that will not let me do development work on my localhost 
server. Some research on this indicates that Oracle does not consider this 
a bug. They consider it a feature!

Anyway, I'm using Java 1.6.0_21, and I recently updated to Firefox 4.0. I 
did not have a problem. I really like FF 4.0 so far. I know I can't keep 
using 1.6.0_21 for an extended period of time, so I'm interested to see 
where this email chain goes.

As to your problem, depending on the Java version that you are using, you 
may need to upgrade or possibly even downgrade!

Otis

--


Otis Rothenberger

Department of Chemistry

Illinois State University
Normal, IL 61790-4160

http://chemagic.org



From: Patrick J. Carroll carro...@sas.upenn.edu
Sent: Saturday, April 02, 2011 8:31 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Help with Firefox 4 

Just installed Firefox 4 on Windows 7 system. Now Java doesn't work!

There was a message during installation that the Java plug-in is 
incompatible
with Firefox 4. So what do I do?

Pat

Patrick J. Carroll, Ph.D.
Director, X-ray Crystallography Facility
Department of Chemistry
University of Pennsylvania
Philadelphia, PA

Phone: 215-898-3505
Web: http://macxray.chem.upenn.edu


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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Bob,

I've tried COLOR RANGE -0.025 0.025 but i got the same surface, with no
color change. I've tried color colorSchemeName RANGE [min] [max] too and
the same thing happened. What am i doing wrong?
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

that's with the ISOSURFACE command? or by itself? You need

isosurface COLOR RANGE .

when creating the isosurface or, after the fact:

color ISOSURFACE range ...

if the isosurface is already created.

On Sat, Mar 12, 2011 at 2:05 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 I've tried COLOR RANGE -0.025 0.025 but i got the same surface, with no
 color change. I've tried color colorSchemeName RANGE [min] [max] too and
 the same thing happened. What am i doing wrong?


 --
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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 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] Help with surfaces

[Robert Hanson]

look for range in the online documentation

http://chemapps.stolaf.edu/jmol/docs/?search=color%20range#isosurfacecolorandcontouroptions

On Thu, Mar 10, 2011 at 10:35 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 Yeah i see that now, thanks. One last question, how can i change the color
 span to absolute values? I wanted min and max values for the surface color
 -0.025 and 0.025.


 --
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-- 
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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] Help with surfaces

[Eduardo Oliveira]

Hi Bob,

Yeah i see that now, thanks. One last question, how can i change the color
span to absolute values? I wanted min and max values for the surface color
-0.025 and 0.025.
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

You have to load the COSMO file, not the MOL file, both for the structure
and the surface. Do you have both the COSMO and the MOL files in some
directory? Just ignore the MOL files, I guess. You could use

Var data = load(?.cosmo)
if (data.find(java.io.FileNotFoundException)) { return }
data = data.split( DATA)

to load that file with a dialog.


Bob

On Fri, Mar 4, 2011 at 5:19 AM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 Actually i didn't generate this .cos files, so i don't know if it was used
 the .mol file and , therefore, i don't know if they were supposed to match.
 But i think for my purpouse it would be easier to avoid creating a .jvxl
 file, since i can use the function loadCosmo and it works. I would like to
 know how to load those commands of the function without opening the console,
 i want, once the .mol is loaded, the surface to open along with it, if it is
 possible. I'm sending the Java class i created attached.


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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 we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d___
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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Bob,

Actually i didn't generate this .cos files, so i don't know if it was used
the .mol file and , therefore, i don't know if they were supposed to match.
But i think for my purpouse it would be easier to avoid creating a .jvxl
file, since i can use the function loadCosmo and it works. I would like to
know how to load those commands of the function without opening the console,
i want, once the .mol is loaded, the surface to open along with it, if it is
possible. I'm sending the Java class i created attached.


JmolTable.java
Description: Binary data


JmolLoadCompound.java
Description: Binary data
--
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

So that makes sense to you that the COSMO and MOL files don't have the same
coordinates? Looks like one is rotated relative to the other.

On Wed, Mar 2, 2011 at 11:06 AM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 Yea i think you're right, kinda pointless generating a .jvxl file. I wanted
 to create the jvxl file because i don't know how to enter that algorithm
 without opening the console window. I wrote a little Java class and i wanted
 it to open the .mol file along with the surface.


 --
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phone: 507-786-3107


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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Bob,

Yea i think you're right, kinda pointless generating a .jvxl file. I wanted
to create the jvxl file because i don't know how to enter that algorithm
without opening the console window. I wrote a little Java class and i wanted
it to open the .mol file along with the surface.
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

By the way, with quaternions and the Jmol compare() function, we could write
a little function that would rotate the isosurface to match any mol file
coordinates.

Bob

On Fri, Feb 25, 2011 at 8:13 AM, Robert Hanson hans...@stolaf.edu wrote:

 Ah, ok. That makes sense. The COSMO file itself must be reloaded, not the
 mol file. I don't know where the COSMO file comes from, but it appears not
 to have come from 1-chlorobutane.mol. (Or, if it did, then some program is
 messing with that file! You need to load the COSMO file itself along with
 the JVXL file. Here's a revised function. Just call it as
 loadCosmo(xxx.cos, false) before issuing the JVXL file. It's not clear to
 me, if you have the COSMO file, why you would want to create a JVXL file.

 Bob


 function loadCosmo(fname, withSurface) {
if ( + withSurface == ) { withSurface = true }  # default TRUE

print reading  + fname
Var fdata = load(fname).split( DATA)
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms.length + segments.length
fdata =  + n + \ndata are from  + fname + \n
print nAtoms =  + atoms.length +  nSegments =  + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] +  -  + radius + \n
}
if (withSurface) {

  for (Var i = 1; i =segments.length; i++) {
  Var sigma = (segments[i])[77][88]
  fdata += Xx  + (segments[i])[17][52] + sigma + \n
  }
  load inline @fdata
  isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
 {_XX} ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
  } else {
  load inline @fdata
  }
 }



 On Thu, Feb 24, 2011 at 6:46 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 I do the following steps:

 1) I load 1-CHLOROBUTANE.mol
 2) I open the console and enter this:

 function loadCosmo(fname) {
print reading  + fname
Var fdata = load(fname).split( DATA)
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms.length + segments.length
fdata =  + n + \ndata are from  + fname + \n
print nAtoms =  + atoms.length +  nSegments =  + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] +  -  + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx  + (segments[i])[17][52] + sigma + \n
}
load inline @fdata

isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
 {_XX} ignore {not _XX} property partialcharge colorscheme rwb

delete _Xx
 }

 loadCosmo 1-CHLOROBUTANE.cos

 3) I obtain picture nº 1
 4) I right click FileSave jvxl surface
 5) I obtain nº 2
 6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
 2.jvxl colorscheme rwb and i get nº3.


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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 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


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] Help with surfaces

[Robert Hanson]

Ah, ok. That makes sense. The COSMO file itself must be reloaded, not the
mol file. I don't know where the COSMO file comes from, but it appears not
to have come from 1-chlorobutane.mol. (Or, if it did, then some program is
messing with that file! You need to load the COSMO file itself along with
the JVXL file. Here's a revised function. Just call it as
loadCosmo(xxx.cos, false) before issuing the JVXL file. It's not clear to
me, if you have the COSMO file, why you would want to create a JVXL file.

Bob


function loadCosmo(fname, withSurface) {
   if ( + withSurface == ) { withSurface = true }  # default TRUE
   print reading  + fname
   Var fdata = load(fname).split( DATA)
   Var atoms = fdata[2].lines[3][-2]
   Var segments = fdata[3].lines[3][0]
   Var n = atoms.length + segments.length
   fdata =  + n + \ndata are from  + fname + \n
   print nAtoms =  + atoms.length +  nSegments =  + segments.length
   for (Var i = 1; i =atoms.length; i++) {
   Var radius = (atoms[i])[52][63]
   fdata += (atoms[i])[6][51] +  -  + radius + \n
   }
   if (withSurface) {
 for (Var i = 1; i =segments.length; i++) {
 Var sigma = (segments[i])[77][88]
 fdata += Xx  + (segments[i])[17][52] + sigma + \n
 }
 load inline @fdata
 isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb
   delete _Xx
 } else {
 load inline @fdata
 }
}



On Thu, Feb 24, 2011 at 6:46 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 I do the following steps:

 1) I load 1-CHLOROBUTANE.mol
 2) I open the console and enter this:

 function loadCosmo(fname) {
print reading  + fname
Var fdata = load(fname).split( DATA)
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms.length + segments.length
fdata =  + n + \ndata are from  + fname + \n
print nAtoms =  + atoms.length +  nSegments =  + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] +  -  + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx  + (segments[i])[17][52] + sigma + \n
}
load inline @fdata

isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
 {_XX} ignore {not _XX} property partialcharge colorscheme rwb

delete _Xx
 }

 loadCosmo 1-CHLOROBUTANE.cos

 3) I obtain picture nº 1
 4) I right click FileSave jvxl surface
 5) I obtain nº 2
 6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
 2.jvxl colorscheme rwb and i get nº3.


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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 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] Help with surfaces

[Eduardo Oliveira]

Hi Bob,

I should've sent a picture to make my explanation clearer. That is what i get.
attachment: 1-CHLOROBUTANE.jpg--
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

nah! Are you sure you made those from the same coordinate file? Can you send
me some files? scripts that were used?

Bob

On Thu, Feb 24, 2011 at 12:03 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Bob,

 I should've sent a picture to make my explanation clearer. That is what i
 get.


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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] Help with surfaces

[Eduardo Oliveira]

Hi Bob,

I do the following steps:

1) I load 1-CHLOROBUTANE.mol
2) I open the console and enter this:

function loadCosmo(fname) {
print reading  + fname
Var fdata = load(fname).split( DATA)
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms.length + segments.length
fdata =  + n + \ndata are from  + fname + \n
print nAtoms =  + atoms.length +  nSegments =  + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] +  -  + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx  + (segments[i])[17][52] + sigma + \n
}
load inline @fdata

isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb

delete _Xx
}

loadCosmo 1-CHLOROBUTANE.cos

3) I obtain picture nº 1
4) I right click FileSave jvxl surface
5) I obtain nº 2
6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
2.jvxl colorscheme rwb and i get nº3.
attachment: 1.jpg

1-CHLOROBUTANE.mol
Description: Binary data
attachment: 3.jpg

2.jvxl
Description: Binary data
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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Robert,

Sorry it took me so long to answer. Your algorithm worked just fine, thank
you!

However, i'm having another trouble now. After the surface is generated
everything is alright, i save it as a .jvxl file, then when i try to load it
to the same molecule, the surface and the molecule don't match, it seems
they have different coordinates. So i would like to know what i'm doing
wrong.
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

I'm certainly not seeing that. I do see that they don't have the rwb
colorscheme. So coming from the JVXL file you need to specify the color
scheme:

isosurface t2.jvxl colorscheme rwb*

*I realize that should not be necessary, but it is. The color scheme used is
not saved with the isosurface in a JVXL file.

You mean they are not matching? I'm certainly not seeing that. See attached
images.

Bob


On Wed, Feb 23, 2011 at 5:08 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Robert,

 Sorry it took me so long to answer. Your algorithm worked just fine, thank
 you!

 However, i'm having another trouble now. After the surface is generated
 everything is alright, i save it as a .jvxl file, then when i try to load it
 to the same molecule, the surface and the molecule don't match, it seems
 they have different coordinates. So i would like to know what i'm doing
 wrong.


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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
attachment: tcosmo.jpgattachment: tjvxl.jpg--
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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Robert,

I think you got it. I just have some questions.  Do these commands
given get the coordinates given by the file .cos? And do these
commands get the points from both sets of data (atomic data and
segment data)? because i'm manly interested on segment data.

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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

OK, I see how to do this.

1) transform your data into what looks like an XYZ file, where the first
part is the actual atoms, and the second part is as set of bogus atoms
positioned where you need them and including the data you want to plot in
the fifth column. I made a little .xyz file using Excel. But you could do it
with Jmol scripting as well. The file looks like this:

227

C -0.19 -0.309948 -0.463554
C 1.328281 -0.309948 -0.463554
C 1.829054 1.110428 -0.463554
C -0.729241 -1.734088 -0.479755
Cl 3.716621 0.988878 -0.443163
H -0.588478 0.23564 0.422575
H -0.588776 0.255435 -1.337048
H 1.723662 -0.86262 0.415297
H 1.724508 -0.861985 -1.342402
H 1.593678 1.690312 -1.36857
H 1.574928 1.697606 0.431649
H -1.828714 -1.759592 -0.479517
H -0.401381 -2.291613 -1.36905
H -0.400229 -2.311819 0.396145
Xx -1.033075 1.479272 -0.28151 -0.001523
Xx -2.098453 0.197779 -0.866198 0.000799
Xx -1.501445 1.182288 -0.589701 -0.001548
Xx -1.991341 0.484824 -0.769458 -0.000396
...
etc.
...

2) load that file.
3) set VDW radii.
4) create an isosurface for the atoms and color it by the partial charge
data in the segment data.
5) delete the unwanted atoms (segment positions).

Here's the script:


load t.xyz

{_H}.vdw = 1.416
{_C}.vdw = 2.006
{_Cl}.vdw = 2.365

isosurface select {not _XX} ignore {_XX} solvent 1.2 map select {_XX} ignore
{not _XX} property partialcharge colorscheme rwb

delete _XX


I think that's about as good as you can do. Could be interesting to
streamline this and allow mapping of any such point-based data. Have to
think about that

Bob



On Sat, Feb 19, 2011 at 5:31 PM, Robert Hanson hans...@stolaf.edu wrote:

 These just use the coordinates from

 load $1-chlorobutane

 Presumably you have a model in some other file, right?

 I see this in the file:

  EPS=999.0 COSWRT RSOLV=1.2 RM1 NSPA=92
 VDW(;H=1.416;C=2.006;N=1.829;O=1.7936;F=
 1.7346;S=2.124;P=2.124;CL=2.365;BR=2.183;I=2.3364) GNORM=0.1 RELSCF=0.1

 OK, I think I see part of what you are after, sort of. I plotted the points
 in the SEGMENT section, and they appear to be points on a VDW surface. Jmol
 can reproduce that surface using

 load $1-chlorobutane
 {_H}.vdw = 1.416
 {_C}.vdw = 2.006
 {_Cl}.vdw = 2.365
 isosurface solvent 1.2

 and every point is on it. Note, by the way, that this is NOT a
 solvent-accessible surface; it's a solvent-excluded surface.

 Q: Is that what you expected -- solvent-excluded, not solvent-accessible?

 Q: These are rather unusual Van der Waals radii. Where do they come from?
 Jmol by default uses H=1.1, C = 1.7, Cl 1.75. Why are these VDW radii so
 large?

 Q: How does a segment have only a point (and not, perhaps, three points)
 and still have an area?

 Q: I see the COSMO-CHARGE column is basically all zeros. What is the
 significance of the SIGMA column?

 I don't have access to Perkin Transactions, so I need your help
 understanding the purpose of these values.


But, basically, I think what you want to do is create a surface that is
based on values at those points. What we need are triangles, not points.
Nothing here gives any clue as to how to connect those dots into triangles?
Jmol doesn't do that by itself. I suppose we could write something that does
that, but
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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 we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
attachment: t.jpg--
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

(oh, by the way, that will require
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip, uploading
now...)

On Sat, Feb 19, 2011 at 7:31 PM, Robert Hanson hans...@stolaf.edu wrote:

 Here you go!

 function loadCosmo(fname) {
 print reading  + fname
 Var fdata = load(fname).split( DATA)
 Var atoms = fdata[2].lines[3][-2]
 Var segments = fdata[3].lines[3][0]
 Var n = atoms.length + segments.length
 fdata =  + n + \ndata are from  + fname + \n
 print nAtoms =  + atoms.length +  nSegments =  + segments.length
 for (Var i = 1; i =atoms.length; i++) {
 Var radius = (atoms[i])[52][63]
 fdata += (atoms[i])[6][51] +  -  + radius + \n
 }
 for (Var i = 1; i =segments.length; i++) {
 Var sigma = (segments[i])[77][88]
 fdata += Xx  + (segments[i])[17][52] + sigma + \n
 }
 load inline @fdata

 isosurface select {not _XX} ignore {_XX} solvent 1.2 map select {_XX}
 ignore {not _XX} property partialcharge colorscheme rwb
 delete _Xx
 }

 loadCosmo xxx.cos




-- 
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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Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

OK, so this is just a file that indicates partial charge, mostly. You could
write a little Jmol script that would map those charges onto a surface.
Something like the following:


Var fileData =
load(xxx.cos).split(SIGMA)[2].split(SEGMENT)[1].trim().lines
Var nLines = fileData.length

for (Var i = 1; i = nLines; i++) {
  {atomno=i}.property_sigma = 0.0 + (fileData[i])[88][0]
}

isosurface molecular map property_sigma translucent

Is that the idea?


Bob


On Thu, Feb 17, 2011 at 6:52 PM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Robert,

 I attached an example to this message. I would like to create a colored
 surface in Jmol using x,y,z coordinates along with the SIGMA data. If there
 is something unclear about the data, just ask me.


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[Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi everyone,

I have some surface data and i would like to generate a colored surface on
Jmol, however the file format i'm using (.cos) is not supported by Jmol. I
would like to know more about the structure of .jvxl files, in order to
convert these files.

Thanks for your help.
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

what are .cos files? What program creates these?

On Thu, Feb 17, 2011 at 7:39 AM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi everyone,

 I have some surface data and i would like to generate a colored surface on
 Jmol, however the file format i'm using (.cos) is not supported by Jmol. I
 would like to know more about the structure of .jvxl files, in order to
 convert these files.

 Thanks for your help.


 --
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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Robert,

.cos files are files which contain data for (x,y,z) coordinates, that can
generate a surface around the molecule. They are created by a program called
MOPAC. If it helps, i could send an attachment with an example of a .cos
file.
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Re: [Jmol-users] Help with surfaces

[Robert Hanson]

yes, please send an example.

On Thu, Feb 17, 2011 at 9:47 AM, Eduardo Oliveira eduardo...@gmail.comwrote:

 Hi Robert,

 .cos files are files which contain data for (x,y,z) coordinates, that can
 generate a surface around the molecule. They are created by a program called
 MOPAC. If it helps, i could send an attachment with an example of a .cos
 file.




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phone: 507-786-3107


If nature does not answer first what we want,
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Re: [Jmol-users] Help with surfaces

[Eduardo Oliveira]

Hi Robert,

I attached an example to this message. I would like to create a colored
surface in Jmol using x,y,z coordinates along with the SIGMA data. If there
is something unclear about the data, just ask me.


1-CHLOROBUTANE.cos
Description: Binary data
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[Jmol-users] help with atom expressions when no chain identifier is specified in the PDB file

[Paul Pillot]

Dear Jmolers,
I'm currently struggling with atom expressions, here is the script :
when the residue I ant to select or deselect is 10:B, this works fine : 
if ({selected or 10:B}.size{selected}.size ) select selected or 10:B; else 
select selected and not 10:B;
But when the residue is for example 10: (no chain identifier), it leads to an 
error :
if ({selected or 10:}.size{selected}.size ) select selected or 10:; else 
select selected and not 10:;

if ({selected or 10:}.size{selected}.size ) 
Erreur du compilateur de script: } attendu

However, select 10: works as expected (to me at least !)

Is there a proper syntax to circumvent this error ?
Thanks
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Re: [Jmol-users] help with atom expressions when no chain identifier is specified in the PDB file

[Angel Herráez]

Hi Paul

Chains with no ID...  yes, I remember hittting that problem once. Not 
sure of what I did in the end, but probably something like 10:? or 
10:*. Problem is that does not exclude 10:A, 10:B etc

If I remember or find the solution, I will tell you.

Meanwhile, maybe try adding extra braces:

 if ({selected or {10:} }.size{selected}.size ) 



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Re: [Jmol-users] help with atom expressions when no chain identifier is specified in the PDB file

[Robert Hanson]

It was a missing line in the script compiler code. Fixed for Jmol 12.0.RC27
and 11.8.26.

Bob

On Tue, Jul 20, 2010 at 8:36 AM, Paul Pillot 
paul.pil...@ac-orleans-tours.fr wrote:

 Dear Jmolers,
 I'm currently struggling with atom expressions, here is the script :
 when the residue I ant to select or deselect is 10:B, this works fine :
 if ({selected or 10:B}.size{selected}.size ) select selected or 10:B; else
 select selected and not 10:B;
 But when the residue is for example 10: (no chain identifier), it leads to
 an error :
 if ({selected or 10:}.size{selected}.size ) select selected or 10:; else
 select selected and not 10:;

 if ({selected or 10:}.size{selected}.size ) 
 Erreur du compilateur de script: } attendu

 However, select 10: works as expected (to me at least !)

 Is there a proper syntax to circumvent this error ?
 Thanks
 -Paul


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[Jmol-users] help needed --- lipophilicity

[Robert Hanson]

I need a volunteer to help me with lipophilicity over the next couple of
days. Jmol 12.0.RC19 will have a new MLP option for isosurface. What I
need to know is:

-- What should be the default distance function? I see several -- 1/d, 1/(1
+ d), e^-d, e^(-d/2). Are there more? Are they all important? These four are
implemented in Jmol now, but I don't exactly see why any one would be better
than any other.

-- What is the preferred color scheme?

-- I need some comparison examples, both in the small molecule and the
biomolecule area. Mostly I'd like to see what other programs do to map a
surface with MLP data. I've tried this a bit with Chime and it just looks so
bad I can't do anything with it. And I've tried it with PyMol using a PQR
file, but I don't see how to adjust PyMol to give me different cutoffs.
(Jmol now has the pyMLP implementation of molecular lipophilic potential.)

Thanks,

Bob





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


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

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Re: [Jmol-users] help needed --- lipophilicity

[Angel Herráez]

Bob, I know nothing about the basis of lipophilicity ither than having seen it 
a couple times in 
Chime, coloring molecular surfaces.

I'll try to check tomorrow some examples in Chime and maybe in Accelrys 
Discovery Studio 
Visualizer too (don't remember now if it offers MLP, but might be, in which 
case that would be 
a good source and comparison).

I see this as (another) great addition to 12.0!!!
The Wikipedia page saying that Jmol was not a full alternative to Chime has its 
days 
counted!   (There was quite an argument over that sentence)




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Re: [Jmol-users] Help with Jmol Math

[Rolf Huehne]

On 02/19/2010 06:20 AM, Otis Rothenberger wrote:
 Hello-
 
 I'm working on an atom append script to click append a C atom (methyl group
 actually) to an existing atom in a Jmol model. The following JavaScript
 function works, but it is far from elegant. I'm fairly sure that there are
 Jmol math approaches to deal with some specific script actions that I'm
 attempting, but I could use some guidance. I'm new to Jmol math. The
 function and my questions:
 
 function appendC(x) {
 var scpt = select;set appendNew false;data 'append'|1|add|At 2 2 2|end
 'append';show data;select astatine;
 scpt += {selected}.element='C';connect (selected)(atomIndex= + x +
 );select *;wireframe 0.15; spacefill 23%;boundbox {*};
 scpt += centerat boundbox;delete hydrogens;minimize addHydrogens;
 jmolScript(scpt, 01);
 }
 
 x is the atomIndex of the clicked atom via a pickCallback function.
 
I think you could define this javascript function also as a Jmol script
function. Then you could use for example the boundbox information more
easily to set the position of the new atom (see below).

 1) The ridiculous addition of astatine relates to my inability to use
 getProperty for the atomIndex of the newly appended atom, so I appended a
 very rare element, selected it, and changed it to carbon. Is there a way to
 get this atomIndex a bit more gracefully?
Isn't the atomIndex just a sequential number? If this is true I would
expect that it will be the current (before the addition) maximum
atomIndex + 1. But I don't know how atom deletions might interfere here.

 
 2) The 2 2 2 coordinates were selected to get the appended atom away from
 existing atoms in ammonia. I'd really like a general approach to get this
 atom outside of the VDW surface of any molecule. I know how to calculate the
 isosurface area if I generate it, but I really don't want a surface painted
 on the screen. Further, I'm not sure the area will help. I could calculate a
 diameter, but in a long molecule, I would still be in trouble. Is there any
 Jmol math approach that will calculate a safe distance for this appended
 atom?
 
You could use the boundbox to determine the outer borders of the
molecule and then add some offset. I use the following script to
determine the boundbox values:

  boundbox_selection_expression = NOT WATER;
  boundbox (@{boundbox_selection_expression});
  bound_box = getProperty(boundboxInfo, vector);
  vector_x  = bound_box.x;
  vector_y  = bound_box.y;
  vector_z  = bound_box.z;


 3) One approach is to really put the appended atom into orbit. The
 coordinates 50 50 50 actually work with ammonia. By using a zoom 2000, you
 can even see the result. The function really works very nicely if you get
 the appended atom away from existing atoms. If you do not, then the minimize
 produces chemical nonsense even though I explicitly connect only the two
 atoms. If this orbit approach turns out to be the best approach, then a
 scaling factor that normalizes molecule size would be useful. One
 possibility is using math with zoom 100 and the orbit coordinates, 50 50 50.
 Is this math doable with zoom? Is there another math approach that can be
 used to redefine zoom 100?
 
I am not sure if I understand what the problem is here.
Is it that you want to display everything except the appended atom at
50 50 50 filling the view?
If this is the problem you could try zoomto (atom expression).

Regards,
Rolf

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Re: [Jmol-users] Help with Jmol Math

[Rolf Huehne]

On 02/19/2010 11:19 AM, Rolf Huehne wrote:
 I am not sure if I understand what the problem is here.
 Is it that you want to display everything except the appended atom at
 50 50 50 filling the view?
 If this is the problem you could try zoomto (atom expression).
 
Sorry, I forgot the important 0 at the end:

zoomto (atom expression) 0

Regards,
Rolf

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Re: [Jmol-users] Help with Jmol Math

[Rolf Huehne]

On 02/19/2010 06:20 AM, Otis Rothenberger wrote:
 1) The ridiculous addition of astatine relates to my inability to use
 getProperty for the atomIndex of the newly appended atom, so I appended a
 very rare element, selected it, and changed it to carbon. Is there a way to
 get this atomIndex a bit more gracefully?
 
You could store all pre-existing atoms in a varaible and after the
addition use this set to select only the new atom:

define old_atoms all
...add atom...
select not old_atoms

Regards,
Rolf

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Re: [Jmol-users] Help with Jmol Math

[Robert Hanson]

On Thu, Feb 18, 2010 at 11:20 PM, Otis Rothenberger o...@chemagic.comwrote:

 Hello-

 I'm working on an atom append script to click append a C atom (methyl group
 actually) to an existing atom in a Jmol model. The following JavaScript
 function works, but it is far from elegant. I'm fairly sure that there are
 Jmol math approaches to deal with some specific script actions that I'm
 attempting, but I could use some guidance. I'm new to Jmol math. The
 function and my questions:

 function appendC(x) {
 var scpt = select;set appendNew false;data 'append'|1|add|At 2 2 2|end
 'append';show data;select astatine;
 scpt += {selected}.element='C';connect (selected)(atomIndex= + x +
 );select *;wireframe 0.15; spacefill 23%;boundbox {*};
 scpt += centerat boundbox;delete hydrogens;minimize addHydrogens;
 jmolScript(scpt, 01);
 }

 x is the atomIndex of the clicked atom via a pickCallback function.

 1) The ridiculous addition of astatine relates to my inability to use
 getProperty for the atomIndex of the newly appended atom, so I appended a
 very rare element, selected it, and changed it to carbon. Is there a way to
 get this atomIndex a bit more gracefully?

 The next atom to be added will have the atomIndex equal to the number of
atoms present originally:

{*}.length



 2) The 2 2 2 coordinates were selected to get the appended atom away from
 existing atoms in ammonia. I'd really like a general approach to get this
 atom outside of the VDW surface of any molecule. I know how to calculate the
 isosurface area if I generate it, but I really don't want a surface painted
 on the screen. Further, I'm not sure the area will help. I could calculate a
 diameter, but in a long molecule, I would still be in trouble. Is there any
 Jmol math approach that will calculate a safe distance for this appended
 atom?


Why not just put it where you want it to go?



 3) One approach is to really put the appended atom into orbit. The
 coordinates 50 50 50 actually work with ammonia. By using a zoom 2000, you
 can even see the result. The function really works very nicely if you get
 the appended atom away from existing atoms. If you do not, then the minimize
 produces chemical nonsense even though I explicitly connect only the two
 atoms. If this orbit approach turns out to be the best approach, then a
 scaling factor that normalizes molecule size would be useful. One
 possibility is using math with zoom 100 and the orbit coordinates, 50 50 50.
 Is this math doable with zoom? Is there another math approach that can be
 used to redefine zoom 100?

 Any help with the above questions would be appreciated.

 Otis

 --
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 http://chemagic.org


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Re: [Jmol-users] Help with Jmol Math

[Otis Rothenberger]

Thanks Bob and Rolf.

{*}.length to get the atomIndex of the appended atom makes the embarrassing
astatine trick go away. It also has some general utility.

Bob, putting the appended atom anywhere in the reach of other atoms seems to
always get it mired in a web of strange bonds after minimize addHydrogens.
This happens even if I omit the delete hydrogens.

I'm also not sure where I want the appended atom in the general case - some
offfset from the clicked atom's coordinates? What I'm doing as an
alternative is placing the appended atom outside the reach of other atoms
and then letting minimize sort it out.

Rolf, I'll pursue the zoom suggestions that you made. The problem is that
zoom 100 seems to be redefined by the absurdly long bond that I'm forming.
Your suggestion may allow me to redefine it again after the minimization.

Writing this just gave me a thought. I wonder if the appended carbon atom is
still being viewed with astatine's radius. That might explain the web of
strange bonds.

Whatever the situation, I have some direction now. Thanks for the help.

Otis

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Re: [Jmol-users] Help with Jmol Math

[Otis Rothenberger]

Bob and Rolf,

A fairly lengthy data list is appended to this email.

It looks like atomIndex assignment has problems with my approach. The
JavaScript function is now:

function appendC(x) {
var scpt = select;var z={*}.length;set appendNew false;data
'append'|1|add|C 5 5 5|end 'append';show data;;
scpt += connect (atomIndex = @{z})(atomIndex= + x + );select
*;wireframe 0.15; spacefill 23%;boundbox {*};
scpt += centerat boundbox;delete hydrogens;minimize addHydrogens;
jmolScript(scpt, 01);
}

Ammonia (starting molfile) to methyamine works fine.

Subsequent methylamine to ethylamine adds the carbon atom, but it will not
connect, nor will it add hydrogens. Checking all three atomInfo's shows the
problem. There is atomIndex confusion with all the deleting and adding going
on. The array lengths are correct, but atomIndex problems start with the
generated methylamaine. They run 0,4,5,6,7,8,9. It looks like deleted H's
are taken out of the counting sequence.

I suspect this was happening in my atom substitution approach which also
deleted H's, but there I was selecting atoms by picking only - not
calculation.

The astatine trick bypassed this problem also, though that's not the reason
that I used it.

Any thoughts?

Otis

Three atomInfo data sets:

atomInfo*Vector[4]
atomInfo[1].elementnitrogen
atomInfo[1].visibletrue
atomInfo[1].model1
atomInfo[1].radius0.7416667
atomInfo[1].visibilityFlags13
atomInfo[1].clickabilityFlags12
atomInfo[1].bondCount3
atomInfo[1].atomno1
atomInfo[1].elemno7
atomInfo[1].z-0.02149
atomInfo[1].y0.47149998
atomInfo[1].x-0.15370001
atomInfo[1].partialCharge-0.3437
atomInfo[1].symN
atomInfo[1].colix-32761
atomInfo[1].spacefill0.3565
atomInfo[1].coord{-0.15370001 0.47149998 -0.02149}
atomInfo[1].color[x3050f8]
atomInfo[1].info[SUBUNIT]1:A.N1 #1
atomInfo[1].atomIndex0
atomInfo[1]._ipt0
atomInfo[1].formalCharge0
atomInfo[2].elementhydrogen
atomInfo[2].visibletrue
atomInfo[2].model1
atomInfo[2].radius0.525
atomInfo[2].visibilityFlags13
atomInfo[2].clickabilityFlags12
atomInfo[2].bondCount1
atomInfo[2].atomno2
atomInfo[2].elemno1
atomInfo[2].z-0.72179997
atomInfo[2].y0.55750006
atomInfo[2].x0.55189997
atomInfo[2].partialCharge0.1146
atomInfo[2].symH
atomInfo[2].colix-32767
atomInfo[2].spacefill0.253
atomInfo[2].coord{0.55189997 0.55750006 -0.72179997}
atomInfo[2].color[xff]
atomInfo[2].info[SUBUNIT]1:A.H2 #2
atomInfo[2].atomIndex1
atomInfo[2]._ipt1
atomInfo[2].formalCharge0
atomInfo[3].elementhydrogen
atomInfo[3].visibletrue
atomInfo[3].model1
atomInfo[3].radius0.525
atomInfo[3].visibilityFlags13
atomInfo[3].clickabilityFlags12
atomInfo[3].bondCount1
atomInfo[3].atomno3
atomInfo[3].elemno1
atomInfo[3].z0.86950004
atomInfo[3].y0.3621
atomInfo[3].x0.2819
atomInfo[3].partialCharge0.1146
atomInfo[3].symH
atomInfo[3].colix-32767
atomInfo[3].spacefill0.253
atomInfo[3].coord{0.2819 0.3621 0.86950004}
atomInfo[3].color[xff]
atomInfo[3].info[SUBUNIT]1:A.H3 #3
atomInfo[3].atomIndex2
atomInfo[3]._ipt2
atomInfo[3].formalCharge0
atomInfo[4].elementhydrogen
atomInfo[4].visibletrue
atomInfo[4].model1
atomInfo[4].radius0.525
atomInfo[4].visibilityFlags13
atomInfo[4].clickabilityFlags12
atomInfo[4].bondCount1
atomInfo[4].atomno4
atomInfo[4].elemno1
atomInfo[4].z-0.2147
atomInfo[4].y-0.3345
atomInfo[4].x-0.70919997
atomInfo[4].partialCharge0.1146
atomInfo[4].symH
atomInfo[4].colix-32767
atomInfo[4].spacefill0.253
atomInfo[4].coord{-0.70919997 -0.3345 -0.2147}
atomInfo[4].color[xff]
atomInfo[4].info[SUBUNIT]1:A.H4 #4
atomInfo[4].atomIndex3
atomInfo[4]._ipt3
atomInfo[4].formalCharge0



atomInfo*Vector[7]
atomInfo[1].elementnitrogen
atomInfo[1].visibletrue
atomInfo[1].model1
atomInfo[1].radius0.7416667
atomInfo[1].visibilityFlags13
atomInfo[1].clickabilityFlags12
atomInfo[1].bondCount3
atomInfo[1].atomno1
atomInfo[1].elemno7
atomInfo[1].z2.0656333
atomInfo[1].y4.430047
atomInfo[1].x1.8383527
atomInfo[1].partialCharge-0.3437
atomInfo[1].symN
atomInfo[1].colix-32761
atomInfo[1].spacefill0.3565
atomInfo[1].coord{1.8383527 4.430047 2.0656333}
atomInfo[1].color[x3050f8]
atomInfo[1].info[SUBUNIT]1:A.N1 #1
atomInfo[1].atomIndex0
atomInfo[1]._ipt0
atomInfo[1].formalCharge0
atomInfo[2].elementcarbon
atomInfo[2].visibletrue
atomInfo[2].model1
atomInfo[2].radius0.8084
atomInfo[2].visibilityFlags13
atomInfo[2].clickabilityFlags12
atomInfo[2].bondCount4
atomInfo[2].atomno1
atomInfo[2].elemno6
atomInfo[2].z3.1071622
atomInfo[2].y4.0599203
atomInfo[2].x2.781368
atomInfo[2].partialCharge0.0

Re: [Jmol-users] Help with Jmol Math

[Rolf Huehne]

Otis Rothenberger schrieb:
 Subsequent methylamine to ethylamine adds the carbon atom, but it will 
 not connect, nor will it add hydrogens. Checking all three atomInfo's 
 shows the problem. There is atomIndex confusion with all the deleting 
 and adding going on. The array lengths are correct, but atomIndex 
 problems start with the generated methylamaine. They run 0,4,5,6,7,8,9. 
 It looks like deleted H's are taken out of the counting sequence.
 
I wwas suspecting that deletions might interfere. That's why I proposed 
(unlike Bob) to determine the current maximum atomIndex and then add 1 
to it. Unless deleted atomIndex numbers are refused this should work.

Have you tried my other proposal to store the old atoms as an atomset 
and use the set to determine the new atom?
This should work in any case.

Regards,
Rolf

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Re: [Jmol-users] Help with Jmol Math

[Otis Rothenberger]

Rolf,

Yup, that seems to work for getting the atomIndex. It just took a while for
me to find the correct dot notation by playing with:

var z={*}.atomIndex.max;echo @z;

I'm new to the math component of Jmol, so I'm doing a lot of trial and error
with math notation right now.

I have not tried your other approach yet because I think it just sunk in as
I read you last note. Did you mean

select{*).

add the carbon atom code here

select unselected

???

Otis



On Fri, Feb 19, 2010 at 2:37 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 Otis Rothenberger schrieb:
  Subsequent methylamine to ethylamine adds the carbon atom, but it will
  not connect, nor will it add hydrogens. Checking all three atomInfo's
  shows the problem. There is atomIndex confusion with all the deleting
  and adding going on. The array lengths are correct, but atomIndex
  problems start with the generated methylamaine. They run 0,4,5,6,7,8,9.
  It looks like deleted H's are taken out of the counting sequence.
 
 I wwas suspecting that deletions might interfere. That's why I proposed
 (unlike Bob) to determine the current maximum atomIndex and then add 1
 to it. Unless deleted atomIndex numbers are refused this should work.

 Have you tried my other proposal to store the old atoms as an atomset
 and use the set to determine the new atom?
 This should work in any case.

 Regards,
 Rolf


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Re: [Jmol-users] Help with Jmol Math

[Rolf Huehne]

Otis Rothenberger schrieb:
 Rolf,
 
 Yup, that seems to work for getting the atomIndex. It just took a while 
 for me to find the correct dot notation by playing with:
 
 var z={*}.atomIndex.max;echo @z;
 
 I'm new to the math component of Jmol, so I'm doing a lot of trial and 
 error with math notation right now.

I wasn't totally sure about the syntax so I didn't want to make a 
specific code proposal.


 I have not tried your other approach yet because I think it just sunk in 
 as I read you last note. Did you mean
 
 select{*).
 
 add the carbon atom code here
 
 select unselected
 
 ???
 
Yes, this would be a similar approach. I just added a storage step 
because I didn't know if the append command would affect the selection.

Regards,
Rolf

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Re: [Jmol-users] Help with Jmol Math

[Robert Hanson]

I think you should always be able to know where the atom is to go. If it
were me, I would always do atom replacement, so when, say, I click on an H
atom, it becomes a CH3. Isn't that the way Spartan does it? I would just
follow their lead on that. No need to reinvent the wheel here.

Bob

On Fri, Feb 19, 2010 at 11:21 AM, Otis Rothenberger o...@chemagic.comwrote:

 Thanks Bob and Rolf.

 {*}.length to get the atomIndex of the appended atom makes the embarrassing
 astatine trick go away. It also has some general utility.

 Bob, putting the appended atom anywhere in the reach of other atoms seems
 to always get it mired in a web of strange bonds after minimize
 addHydrogens. This happens even if I omit the delete hydrogens.

 I'm also not sure where I want the appended atom in the general case - some
 offfset from the clicked atom's coordinates? What I'm doing as an
 alternative is placing the appended atom outside the reach of other atoms
 and then letting minimize sort it out.

 Rolf, I'll pursue the zoom suggestions that you made. The problem is that
 zoom 100 seems to be redefined by the absurdly long bond that I'm forming.
 Your suggestion may allow me to redefine it again after the minimization.

 Writing this just gave me a thought. I wonder if the appended carbon atom
 is still being viewed with astatine's radius. That might explain the web of
 strange bonds.

 Whatever the situation, I have some direction now. Thanks for the help.


 Otis

 --
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 http://chemagic.org


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phone: 507-786-3107


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it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] Help with Jmol Math

[Otis Rothenberger]

Hello-

I'm working on an atom append script to click append a C atom (methyl group
actually) to an existing atom in a Jmol model. The following JavaScript
function works, but it is far from elegant. I'm fairly sure that there are
Jmol math approaches to deal with some specific script actions that I'm
attempting, but I could use some guidance. I'm new to Jmol math. The
function and my questions:

function appendC(x) {
var scpt = select;set appendNew false;data 'append'|1|add|At 2 2 2|end
'append';show data;select astatine;
scpt += {selected}.element='C';connect (selected)(atomIndex= + x +
);select *;wireframe 0.15; spacefill 23%;boundbox {*};
scpt += centerat boundbox;delete hydrogens;minimize addHydrogens;
jmolScript(scpt, 01);
}

x is the atomIndex of the clicked atom via a pickCallback function.

1) The ridiculous addition of astatine relates to my inability to use
getProperty for the atomIndex of the newly appended atom, so I appended a
very rare element, selected it, and changed it to carbon. Is there a way to
get this atomIndex a bit more gracefully?

2) The 2 2 2 coordinates were selected to get the appended atom away from
existing atoms in ammonia. I'd really like a general approach to get this
atom outside of the VDW surface of any molecule. I know how to calculate the
isosurface area if I generate it, but I really don't want a surface painted
on the screen. Further, I'm not sure the area will help. I could calculate a
diameter, but in a long molecule, I would still be in trouble. Is there any
Jmol math approach that will calculate a safe distance for this appended
atom?

3) One approach is to really put the appended atom into orbit. The
coordinates 50 50 50 actually work with ammonia. By using a zoom 2000, you
can even see the result. The function really works very nicely if you get
the appended atom away from existing atoms. If you do not, then the minimize
produces chemical nonsense even though I explicitly connect only the two
atoms. If this orbit approach turns out to be the best approach, then a
scaling factor that normalizes molecule size would be useful. One
possibility is using math with zoom 100 and the orbit coordinates, 50 50 50.
Is this math doable with zoom? Is there another math approach that can be
used to redefine zoom 100?

Any help with the above questions would be appreciated.

Otis

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Re: [Jmol-users] help displaying jvxl MO

[Robert Hanson]

Bob, I'll be very interested in seeing what you end up with. A couple more
thoughts on this

I did some tests, and there are two problems. First, the data are definitely
mangled. I see escape sequences that should not be there -- \/ -- (escape
FORWARD slash) for example, and there must be something else wrong, because
what is happening is that the first cryptic line, which represents the
position of the edges of the triangles, is too short, so Jmol is going to
the next line (the color line, which in this case just indicates no color)
and reading that. Then it runs out of data on the color line and chokes. I
find no problem reading JVXL files written by 11.6.21 (I don't have 11.6.15
here) and no notes relating to bug fixes, so I think there's no problem with
the ORIGINAL JVXL file. Something along the way of getting it into the
database and back out has mangled it or possibly something in gmail wrecked
it. I don't know.

Yes, the WebMO .MO file would be FAR better to save in the database, because
it preserves all the other useful information.

Also, there's a bug in Jmol that doesn't let it read isosurface data from
the inline string. The following WOULD be the way to read that file if that
bug were not there:

jmolAppletInline(300,getMol(),isosurface ''; )

(that's isosurface single-quote single-quote)

In other words, load the model inline and then read the isosurface from the
file that was loaded.

That will work in the next version of Jmol. But you won't need it if you use
the MO file. With that you would just use:

jmolAppletInline(300,getMol(),mo 1)

and if there are multiple MOs in the file, then you can get all of them in
the right-click menu, and you can enumerate them on your page using:

jmolAppletInline(300,getMol(),mo 1;javascript 'fileLoaded()'; )

and then, in JavaScript:

function fileLoaded() {
 var  mos = jmolGetPropertyAsArray(auxiliaryInfo.models[1].moData.mos)
  alert(mos.length +  molecular orbitals were loaded)
  for (var i = 0; i  mos.length; i++) {
alert(mos[i].energy)
  }
}

The auxiliaryInfo property has data like this:

auxiliaryinfo.models[1].moData.mos*Vector[1]
auxiliaryinfo.models[1].moData.mos[1].occupancy2.0
auxiliaryinfo.models[1].moData.mos[1].energy-0.42780003
auxiliaryinfo.models[1].moData.calculationType?
auxiliaryinfo.models[1].moData.energyUnitseV

[Note that in JavaScript you have to reduce those indexes by 1 because Jmol
starts with [1] and goes through [0] (so you can always pick up the last
element with [0] or the next to last with [-1], etc.]

You have to be a little careful there, as indicated, so that you do not try
to access file information until the applet is downloaded and the model file
is loaded. Here's the generic way to do that that also shows how you can
display all the auxiliary info that came with the file:

head
function getMol() { return some valid model file data }

function fileLoaded() {
 var  info = jmolGetPropertyAsString(auxiliaryInfo)
 document.getElementById(outputdiv).innerHTML = pre + info + pre;
}

/script
/headbody
script type=text/javascript
jmolAppletInline(300,getMol(),javascript fileLoaded())
/script
div id=outputdiv/div
/body
/html


My point is simply that you can easily pull out the information in the .MO
file that could be useful in the web page presentation.

Good luck!

Bob

On Sat, Jan 23, 2010 at 11:59 PM, Grossman, Robert B 
robert.gross...@uky.edu wrote:

 Ah, I see.  And the .jvxl file that my friend sent me must have been
 created by Jmol from a QM calculation that my friend had generated with
 WebMO and loaded into Jmol.  So when he was trying to make my life easier by
 sending me the .jvxl file instead of the WebMO results file, he was really
 making it more difficult, because I was loading the data inline, and Jmol
 couldn't read the isosurface data in the .jvxl file.

 It all becomes much clearer now...

 It seems the best solution for us is just to store the QM results file into
 the database, deliver the data inline to Jmol, and use scripts and the
 Javascript library to have Jmol generate the MOs.  It achieves all our
 goals.

 Thanks for your patient explanations.


 On 1/23/10 11:34 PM, Robert Hanson hans...@stolaf.edu wrote:



 On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B 
 robert.gross...@uky.edu wrote:
 We can let Jmol create the MO from the QM data in the browser - I think
 that is what we are doing now with the .mo file - but we greatly prefer to
 read the QM data from the database, not from a file.

 I'm still trying to understand the mutual dependencies among load,
 isosurface, and mo.

 When I use jmolLoadInline() with the contents of the .mo file, I can see
 the structure, and I can use the script mo (as implemented by the
 jmolMenu() JS command) to display the MOs.


 By .MO file, not sure what you mean there, unless that's a WebMO file. The
 fact that  you can use the MO command indicates that you are creating the
 orbitals from the basis functions and 

Re: [Jmol-users] help displaying jvxl MO

[Robert Hanson]

Well, two things. First, you must have mangled the data some way - or at
least clipping from this page doesn't work. Because the attached file did
run. Second, you can only load an isosurface inline like that in the very
latest version of Jmol. (I'm not sure it's even in the one I have up at
http://chemapps.stolaf.edu) What you would need to do is (all Jmol script
here)

isosurface INLINE @{javascript(getMol())}

that tells Jmol to read the output of the JavaScript getMol() function as
the data for the isosurface instead of reading the data from a file.

Any reason you don't want to have that data in a file? -- or is this coming
back from a server and you are trying to keep it all together? Sure would be
simpler:

isosurface somefile.jvxl

Bob



On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B robert.gross...@uky.edu
 wrote:

 Hi,

 I have a JVXL file containing MO data that I am trying to display.  I can
 see the molecule, but I can't see the MO.  I have tried various scripts to
 turn on the MO, to no avail.  Below I have copied the relevant part of my
 Web page.  I am using 'mo HOMO;' as the script, but I have tried several
 other commands, including none, to no avail.  How do I display the MO?  Does
 the fact that I load inline prevent the MO from being displayed?

 -- Bob

 script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15
  2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028,
 -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:



-- 
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] help displaying jvxl MO

[Grossman, Robert B]

Hi Bob,

The information is read from an Oracle database and written into a JSP page.  
We have the ability to write information to files, but we want very much to 
avoid having to do it.   We also want to avoid having to deal with multiple 
files to display a single molecule and its associated MOs.  From my point of 
view, Jmol's preference for loading information from files is a real drawback.

We worked around the problem by using a .mo file instead of a .jvxl file.  We 
were able to load the .mo file inline and display its MOs without any problem.  
A friend gave us the proper Jmol JS commands to use to display the MOs.  
jmolMenu([['mo delete;','none'],['mo 3',3],['mo 4',4] ...]); . No 
isosurface commands.

I don't think that we could have mangled the .jvxl information because the .mo 
information, which was loaded and transmitted in exactly the same way, was not 
mangled.  But I could be wrong.

So is it correct that we use isosurface to load MOs into Jmol, and we use 
mo to induce Jmol to display them?

-- Bob

On 1/23/10 5:44 PM, Robert Hanson hans...@stolaf.edu wrote:

Well, two things. First, you must have mangled the data some way - or at least 
clipping from this page doesn't work. Because the attached file did run. 
Second, you can only load an isosurface inline like that in the very latest 
version of Jmol. (I'm not sure it's even in the one I have up at 
http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here)

isosurface INLINE @{javascript(getMol())}

that tells Jmol to read the output of the JavaScript getMol() function as the 
data for the isosurface instead of reading the data from a file.

Any reason you don't want to have that data in a file? -- or is this coming 
back from a server and you are trying to keep it all together? Sure would be 
simpler:

isosurface somefile.jvxl

Bob



On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B robert.gross...@uky.edu 
wrote:
Hi,

I have a JVXL file containing MO data that I am trying to display.  I can see 
the molecule, but I can't see the MO.  I have tried various scripts to turn on 
the MO, to no avail.  Below I have copied the relevant part of my Web page.  I 
am using 'mo HOMO;' as the script, but I have tried several other commands, 
including none, to no avail.  How do I display the MO?  Does the fact that I 
load inline prevent the MO from being displayed?

-- Bob

script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15  2008-11-24 
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, 
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:



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Re: [Jmol-users] help displaying jvxl MO

[Robert Hanson]

I think it just got mangled as being part of the email.

isosurface is used to create MOs from files that are not QM files. --
surfaces.
mo is used to generate the MO data directly from the basis functions. Most
people these days, I think, just let Jmol read the QM file and create the MO
in the browser -- no need for a server end. Are you certain you can't do
that?

Bob

On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B robert.gross...@uky.edu
 wrote:

 Hi Bob,

 The information is read from an Oracle database and written into a JSP
 page.  We have the ability to write information to files, but we want very
 much to avoid having to do it.   We also want to avoid having to deal with
 multiple files to display a single molecule and its associated MOs.  From my
 point of view, Jmol's preference for loading information from files is a
 real drawback.

 We worked around the problem by using a .mo file instead of a .jvxl file.
  We were able to load the .mo file inline and display its MOs without any
 problem.  A friend gave us the proper Jmol JS commands to use to display the
 MOs.  jmolMenu([['mo delete;','none'],['mo 3',3],['mo 4',4] ...]); . No
 isosurface commands.

 I don't think that we could have mangled the .jvxl information because the
 .mo information, which was loaded and transmitted in exactly the same way,
 was not mangled.  But I could be wrong.

 So is it correct that we use isosurface to load MOs into Jmol, and we use
 mo to induce Jmol to display them?

 -- Bob

 On 1/23/10 5:44 PM, Robert Hanson hans...@stolaf.edu wrote:

 Well, two things. First, you must have mangled the data some way - or at
 least clipping from this page doesn't work. Because the attached file did
 run. Second, you can only load an isosurface inline like that in the very
 latest version of Jmol. (I'm not sure it's even in the one I have up at
 http://chemapps.stolaf.edu) What you would need to do is (all Jmol script
 here)

 isosurface INLINE @{javascript(getMol())}

 that tells Jmol to read the output of the JavaScript getMol() function as
 the data for the isosurface instead of reading the data from a file.

 Any reason you don't want to have that data in a file? -- or is this coming
 back from a server and you are trying to keep it all together? Sure would be
 simpler:

 isosurface somefile.jvxl

 Bob



 On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B 
 robert.gross...@uky.edu wrote:
 Hi,

 I have a JVXL file containing MO data that I am trying to display.  I can
 see the molecule, but I can't see the MO.  I have tried various scripts to
 turn on the MO, to no avail.  Below I have copied the relevant part of my
 Web page.  I am using 'mo HOMO;' as the script, but I have tried several
 other commands, including none, to no avail.  How do I display the MO?  Does
 the fact that I load inline prevent the MO from being displayed?

 -- Bob

 script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15
  2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028,
 -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:




 --
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 Conference
 attendees to learn about information security's most important issues
 through
 interactions with peers, luminaries and emerging and established companies.
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St. Olaf College
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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] help displaying jvxl MO

[Grossman, Robert B]

We can let Jmol create the MO from the QM data in the browser - I think that is 
what we are doing now with the .mo file - but we greatly prefer to read the QM 
data from the database, not from a file.

I'm still trying to understand the mutual dependencies among load, isosurface, 
and mo.

When I use jmolLoadInline() with the contents of the .mo file, I can see the 
structure, and I can use the script mo (as implemented by the jmolMenu() JS 
command) to display the MOs.

When I use jmolLoadInline() with the contents of the .jvxl file, I can see 
the structure, but I cannot find a script that will display the isosurface.  Is 
there a script that will display the isosurface after I load it into Jmol with 
jmolLoadInline()?



On 1/23/10 8:39 PM, Robert Hanson hans...@stolaf.edu wrote:

I think it just got mangled as being part of the email.

isosurface is used to create MOs from files that are not QM files. -- surfaces.
mo is used to generate the MO data directly from the basis functions. Most 
people these days, I think, just let Jmol read the QM file and create the MO in 
the browser -- no need for a server end. Are you certain you can't do that?

Bob

On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B robert.gross...@uky.edu 
wrote:
Hi Bob,

The information is read from an Oracle database and written into a JSP page.  
We have the ability to write information to files, but we want very much to 
avoid having to do it.   We also want to avoid having to deal with multiple 
files to display a single molecule and its associated MOs.  From my point of 
view, Jmol's preference for loading information from files is a real drawback.

We worked around the problem by using a .mo file instead of a .jvxl file.  We 
were able to load the .mo file inline and display its MOs without any problem.  
A friend gave us the proper Jmol JS commands to use to display the MOs.  
jmolMenu([['mo delete;','none'],['mo 3',3],['mo 4',4] ...]); . No 
isosurface commands.

I don't think that we could have mangled the .jvxl information because the .mo 
information, which was loaded and transmitted in exactly the same way, was not 
mangled.  But I could be wrong.

So is it correct that we use isosurface to load MOs into Jmol, and we use 
mo to induce Jmol to display them?

-- Bob

On 1/23/10 5:44 PM, Robert Hanson hans...@stolaf.edu wrote:

Well, two things. First, you must have mangled the data some way - or at least 
clipping from this page doesn't work. Because the attached file did run. 
Second, you can only load an isosurface inline like that in the very latest 
version of Jmol. (I'm not sure it's even in the one I have up at 
http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here)

isosurface INLINE @{javascript(getMol())}

that tells Jmol to read the output of the JavaScript getMol() function as the 
data for the isosurface instead of reading the data from a file.

Any reason you don't want to have that data in a file? -- or is this coming 
back from a server and you are trying to keep it all together? Sure would be 
simpler:

isosurface somefile.jvxl

Bob



On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B robert.gross...@uky.edu 
wrote:
Hi,

I have a JVXL file containing MO data that I am trying to display.  I can see 
the molecule, but I can't see the MO.  I have tried various scripts to turn on 
the MO, to no avail.  Below I have copied the relevant part of my Web page.  I 
am using 'mo HOMO;' as the script, but I have tried several other commands, 
including none, to no avail.  How do I display the MO?  Does the fact that I 
load inline prevent the MO from being displayed?

-- Bob

script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15  2008-11-24 
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, 
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:



--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
___