Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Philip Bays
yep. Thanks


On Apr 12, 2010, at 2:34 PM, Robert Hanson wrote:

> Phil, this is probably just a caching problem within your browsers. I've been 
> uploading revised versions all weekend long, and this sounds a lot like what 
> the capabilities were a few days ago. I just added the capability to load the 
> structure there this morning. Yesterday when you clicked on the image you got 
> a blank JME window; today you should see the structure. It's working fine on 
> my Mac using Safari or Firefox.
> 
> Bob
> 
> 
> On Mon, Apr 12, 2010 at 12:05 PM, Philip Bays  wrote:
> Bob: I am really impressed with this capability!!  However, I have a couple 
> of issues on the mac side of things.
> 
> When I use Firefox, Camino, or SeaMonkey I get an error message when loading 
> JME:  The structure you have in there will not load.   But I can use them to 
> correctly generate structures and load them into Jmol.
> 
> With Safari, I can use your structure or my own and get the Jmol structure, 
> but in this case none of the wedge or dashed bonds in the JME structure show 
> connections in the Jmol structure.  They are apparently there because nothing 
> goes flying off into space on minimization, but the bonds are not visible,   
> And in some cases there are extra bonds to hydrogens (three membered rings 
> containing hydrogen.)
> 
> Phil
> 
> On Apr 12, 2010, at 11:38 AM, Robert Hanson wrote:
> 
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>> 
>> now smoothly integrates JME with Jmol. Still two applets -- just shows how 
>> to use JME as a quick input mechanism. Also uses Jmol to read the files that 
>> JME can then display. Question: does JME allow direct file reading, or it is 
>> only reading strings of data? If the latter, well, now it reads files.
>> 
>> Bob
>> 
>> 
>> On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick  
>> wrote:
>> 
>> Yes, very cool and easy to use, perhaps too easy?
>> 
>> My concern is the limitations of the minimisation which will lead to high 
>> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair, 
>> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per 
>> se but could be misleading.
>> 
>> Otherwise works nicely.
>> 
>> 
>> All the best
>> Nick
>> --
>> 3D Organic Animations http://www.chemtube3d.com
>> Tel: +44 (0)151-794-3506 (3500 secretary)
>> 
>> 
>> Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
>> To: jmol-users@lists.sourceforge.net
>> Message-ID:
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> OK! Here we go! Super simple 2D to 3D.
>> 
>> The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5
>> addition of reading bond stereochemistry, Jmol now does a pretty decent job
>> of translating 2D into 3D -- admittedly this is not going to solve all
>> problems, but give it a try:
>> 
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>> 
>> Cool, eh?
>> --
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> ___
>> 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
>> --
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listi

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Robert Hanson
Phil, this is probably just a caching problem within your browsers. I've
been uploading revised versions all weekend long, and this sounds a lot like
what the capabilities were a few days ago. I just added the capability to
load the structure there this morning. Yesterday when you clicked on the
image you got a blank JME window; today you should see the structure. It's
working fine on my Mac using Safari or Firefox.

Bob


On Mon, Apr 12, 2010 at 12:05 PM, Philip Bays  wrote:

> Bob: I am really impressed with this capability!!  However, I have a couple
> of issues on the mac side of things.
>
> When I use Firefox, Camino, or SeaMonkey I get an error message when
> loading JME:  The structure you have in there will not load.   But I can use
> them to correctly generate structures and load them into Jmol.
>
> With Safari, I can use your structure or my own and get the Jmol structure,
> but in this case none of the wedge or dashed bonds in the JME structure show
> connections in the Jmol structure.  They are apparently there because
> nothing goes flying off into space on minimization, but the bonds are not
> visible,   And in some cases there are extra bonds to hydrogens (three
> membered rings containing hydrogen.)
>
> Phil
>
> On Apr 12, 2010, at 11:38 AM, Robert Hanson wrote:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>
> now smoothly integrates JME with Jmol. Still two applets -- just shows how
> to use JME as a quick input mechanism. Also uses Jmol to read the files that
> JME can then display. Question: does JME allow direct file reading, or it is
> only reading strings of data? If the latter, well, now it reads files.
>
> Bob
>
>
> On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick 
> wrote:
>
>>
>> Yes, very cool and easy to use, perhaps too easy?
>>
>> My concern is the limitations of the minimisation which will lead to high
>> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair,
>> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per
>> se but could be misleading.
>>
>> Otherwise works nicely.
>>
>>
>> All the best
>> Nick
>> --
>> 3D Organic Animations http://www.chemtube3d.com
>> Tel: +44 (0)151-794-3506 (3500 secretary)
>>
>>
>> Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
>> To: jmol-users@lists.sourceforge.net
>> Message-ID:
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> OK! Here we go! Super simple 2D to 3D.
>>
>> The JME-Jmol connection has gone unused for too long. With today's
>> 12.0.RC5
>> addition of reading bond stereochemistry, Jmol now does a pretty decent
>> job
>> of translating 2D into 3D -- admittedly this is not going to solve all
>> problems, but give it a try:
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>>
>> Cool, eh?
>>
>> --
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> ___
>> 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
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
>
> http://p.sf.net/sfu/intel-sw-dev___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> (574) 284-4663
> pb...@saintmarys.edu
>
>
>
>
>
> -

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Philip Bays
Bob: I am really impressed with this capability!!  However, I have a couple of 
issues on the mac side of things.

When I use Firefox, Camino, or SeaMonkey I get an error message when loading 
JME:  The structure you have in there will not load.   But I can use them to 
correctly generate structures and load them into Jmol.

With Safari, I can use your structure or my own and get the Jmol structure, but 
in this case none of the wedge or dashed bonds in the JME structure show 
connections in the Jmol structure.  They are apparently there because nothing 
goes flying off into space on minimization, but the bonds are not visible,   
And in some cases there are extra bonds to hydrogens (three membered rings 
containing hydrogen.)

Phil

On Apr 12, 2010, at 11:38 AM, Robert Hanson wrote:

> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
> 
> now smoothly integrates JME with Jmol. Still two applets -- just shows how to 
> use JME as a quick input mechanism. Also uses Jmol to read the files that JME 
> can then display. Question: does JME allow direct file reading, or it is only 
> reading strings of data? If the latter, well, now it reads files.
> 
> Bob
> 
> 
> On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick  
> wrote:
> 
> Yes, very cool and easy to use, perhaps too easy?
> 
> My concern is the limitations of the minimisation which will lead to high 
> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair, 
> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per 
> se but could be misleading.
> 
> Otherwise works nicely.
> 
> 
> All the best
> Nick
> --
> 3D Organic Animations http://www.chemtube3d.com
> Tel:         +44 (0)151-794-3506 (3500 secretary)
> 
> 
> Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
> To: jmol-users@lists.sourceforge.net
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> OK! Here we go! Super simple 2D to 3D.
> 
> The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5
> addition of reading bond stereochemistry, Jmol now does a pretty decent job
> of translating 2D into 3D -- admittedly this is not going to solve all
> problems, but give it a try:
> 
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
> 
> Cool, eh?
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> 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
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
pb...@saintmarys.edu



--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
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Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Otis Rothenberger
Oops, I missed an important point. I just checked Peter Ertl's 
documentation. There is also a molfile string reader function:


readMolFile(String molFile)


Otis


On 4/12/2010 12:09 PM, Robert Hanson wrote:
So to get JME to read files, just have Jmol read the file and pass the 
string to JME.


JME.readMolecule(jmolEvaluate('load('" + filename + '")'))

Bob

On Mon, Apr 12, 2010 at 11:01 AM, Otis Rothenberger 
mailto:osrot...@chemagic.com>> wrote:


Bob,

I think it only reads strings. Implied in your note is the use of the
following JME function via Live Connect:

readMolecule(JME String)

The set minimizationSilent is a big plus. Thank you for that one. I'll
need to get the latest version to check it out, but it sounds like the
molecular wiggle is gone!

Otis

.net/lists/listinfo/jmol-users
   


--
Otis Rothenberger
chemagic.com

--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Robert Hanson
So to get JME to read files, just have Jmol read the file and pass the
string to JME.

JME.readMolecule(jmolEvaluate('load('" + filename + '")'))

Bob

On Mon, Apr 12, 2010 at 11:01 AM, Otis Rothenberger
wrote:

> Bob,
>
> I think it only reads strings. Implied in your note is the use of the
> following JME function via Live Connect:
>
> readMolecule(JME String)
>
> The set minimizationSilent is a big plus. Thank you for that one. I'll
> need to get the latest version to check it out, but it sounds like the
> molecular wiggle is gone!
>
> Otis
>
> On 4/12/2010 11:38 AM, Robert Hanson wrote:
> > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
> >
> > now smoothly integrates JME with Jmol. Still two applets -- just shows
> > how to use JME as a quick input mechanism. Also uses Jmol to read the
> > files that JME can then display. Question: does JME allow direct file
> > reading, or it is only reading strings of data? If the latter, well,
> > now it reads files.
> >
> > Bob
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> 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
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Otis Rothenberger
Bob,

I think it only reads strings. Implied in your note is the use of the 
following JME function via Live Connect:

readMolecule(JME String)

The set minimizationSilent is a big plus. Thank you for that one. I'll 
need to get the latest version to check it out, but it sounds like the 
molecular wiggle is gone!

Otis

On 4/12/2010 11:38 AM, Robert Hanson wrote:
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>
> now smoothly integrates JME with Jmol. Still two applets -- just shows 
> how to use JME as a quick input mechanism. Also uses Jmol to read the 
> files that JME can then display. Question: does JME allow direct file 
> reading, or it is only reading strings of data? If the latter, well, 
> now it reads files.
>
> Bob

-- 
Otis Rothenberger
chemagic.com




--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Robert Hanson
sorry -- meant to respond there...

Nick - that is a perfectly good point. Obviously a 2D representation is
ambiguous with regard to conformation. So that's a limitation. I've put in
some minimal checks, but it is still going to be an issue.
Particularly with cyclohexane conformations you might get odd results as you
mention.

Bob



> On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick 
> wrote:
>
>>
>> Yes, very cool and easy to use, perhaps too easy?
>>
>> My concern is the limitations of the minimisation which will lead to high
>> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair,
>> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per
>> se but could be misleading.
>>
>> Otherwise works nicely.
>>
>>
>>

-- 
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
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
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Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-12 Thread Robert Hanson
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

now smoothly integrates JME with Jmol. Still two applets -- just shows how
to use JME as a quick input mechanism. Also uses Jmol to read the files that
JME can then display. Question: does JME allow direct file reading, or it is
only reading strings of data? If the latter, well, now it reads files.

Bob


On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick wrote:

>
> Yes, very cool and easy to use, perhaps too easy?
>
> My concern is the limitations of the minimisation which will lead to high
> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair,
> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per
> se but could be misleading.
>
> Otherwise works nicely.
>
>
> All the best
> Nick
> --
> 3D Organic Animations http://www.chemtube3d.com
> Tel:     +44 (0)151-794-3506 (3500 secretary)
>
>
> Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
> To: jmol-users@lists.sourceforge.net
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> OK! Here we go! Super simple 2D to 3D.
>
> The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5
> addition of reading bond stereochemistry, Jmol now does a pretty decent job
> of translating 2D into 3D -- admittedly this is not going to solve all
> problems, but give it a try:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>
> Cool, eh?
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> 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
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
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[Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-11 Thread Greeves, Nick

Yes, very cool and easy to use, perhaps too easy?

My concern is the limitations of the minimisation which will lead to high 
energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair, 
biphenyl is flat, simple amides are not planar. This is not Jmol's fault per se 
but could be misleading.

Otherwise works nicely.


All the best
Nick
-- 
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)


Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
To: jmol-users@lists.sourceforge.net
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

OK! Here we go! Super simple 2D to 3D.

The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5
addition of reading bond stereochemistry, Jmol now does a pretty decent job
of translating 2D into 3D -- admittedly this is not going to solve all
problems, but give it a try:

http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

Cool, eh?
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-11 Thread William Reusch
Very nice indeed!  Bob, you are close to forcing me to upgrade the  
version of Jmol I am now using.


Bill





On Apr 11, 2010, at 12:52 AM, Robert Hanson wrote:


OK! Here we go! Super simple 2D to 3D.

The JME-Jmol connection has gone unused for too long. With today's  
12.0.RC5 addition of reading bond stereochemistry, Jmol now does a  
pretty decent job of translating 2D into 3D -- admittedly this is  
not going to solve all problems, but give it a try:


http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

Cool, eh?

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.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
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[Jmol-users] well, what do you know? Jmol and JME 2D to 3D

2010-04-10 Thread Robert Hanson
OK! Here we go! Super simple 2D to 3D.

The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5
addition of reading bond stereochemistry, Jmol now does a pretty decent job
of translating 2D into 3D -- admittedly this is not going to solve all
problems, but give it a try:

http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

Cool, eh?

Bob

-- 
Robert M. Hanson
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St. Olaf College
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phone: 507-786-3107


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