Re: [Jmol-users] Console Again

[Robert Hanson]

JSmol has custom event handling to set and move all windows created as
"draggable", such as the console frame and image frames. If you feel you
must modify this behavior, you should

1) replace JSmol.min.js with js/JSmol.full.js
2) find in that file references to "draggable"
3) play to your heart's content

Note that this action voids your warranty. ;)


Bob

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Re: [Jmol-users] iSpartan files and a question

[Robert Hanson]

Looks to me that you need to use a .sparchive file, not .spartan, if you
want orbitals. The charge business is fixed; if you want to use Mulliken
charges, that can be done with

LOAD ... filter "charge=mulliken"

I've also just added

LOAD ... filter "natcharge"

just for you, Otis. ;)

Bob



On Wed, Jul 26, 2017 at 10:05 PM, Otis Rothenberger 
wrote:

> Bob,
>
> I decided to pull the charges out of the iSpartan files using Jmol's
> javascript getPropertyAsString with fileContent after the spartan file is
> loaded. This allows me to provide users with the ability to 3-way "toggle"
> MULCHARGES, ESPCHARGES, and NATCHARGES without reload of the model. The
> student user at Bradley is using this to study partial charges, so the
> "toggle" is a nice feature for her.
>
> The difference between my old spartan files and these new spartan files,
> iSpartan AND files from the latest version of "big" Spartan in use at
> Bradley University, is the number of spaces after the "PROP" markers!!! I
> made the old and new files compatible by parsing the files with regular
> expression splits.
>
> My next question with all of this is about MO data. I see now that what
> iSpartan is doing is providing limited MO data - HOMO, LUMO, and a few
> other MO's close to HOMO and LUMO.
>
> Here's a link to the text version of the iSpartan file for ethylene:
>
> http://chemagic.org/ethylene.txt
>
> Is there any chance of pulling HOMO and LOMO surfaces out to this file
> once it's loaded in Jmol via the aforementioned approach I used for charge?
>
> While the student at Bradley got me started on this, it seems to me that
> iSpartan is a very nice low budget way to access spartan files that might
> be of interest to my secondary school low budget users.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
>
> 
> --
> Check out the vibrant tech community on one of the world's most
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>



-- 
Robert M. Hanson
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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Re: [Jmol-users] Jmol Tutorial Manual now online and accessible

[Robert Hanson]

 Absolutely fantastic, Jeff. It is really rewarding to see such extensive
effort involving Jmol to make it possible for students to better understand
biochemistry. Wow.

The only thing I might add is that one no longer needs Jmol.jar. You might
consider mentioning at the top that what you are suggesting can be done at
the RCSB site itself, by opening a console, and that any site with JSmol
such as https://chemapps.stolaf.edu/jmol/jsmol/simple.htm can load PDB
files simply by drag-dropping a PDB file into it.

Bob
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Re: [Jmol-users] installing JSmol extension

[Robert Hanson]

I did just copy that link from my developer console report. The way you had
that:

 http://dipc.ehu.es/bondslam/index.php/Hypervalence

for the page and then

images/b/b4/CH3F_mo10.cub.jvxl



for the object meant that the browser put  that together as

 http://dipc.ehu.es/bondslam/index.php/images/b/b4/CH3F_mo10.cub.jvxl

That's all. I think you also could probably have use
../images/b/b4/CH3F_mo10.cub.jvxl

Anyway, it was just returning a "file not found" sort of page rather than
the real thing, and then the odd UNKNOWN reader issue just wasn't clearly
indicating what the problem was.

Bob





On Tue, Jul 25, 2017 at 12:41 PM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:

> Yes. And the surface looks great.
>
> Note: if you want to avoid the simplified rendering of the surface while
> rotating the model, you may add 8 to the 
> block.
>
> This sets platformSpeed as defined at https://chemapps.stolaf.edu/
> jmol/docs/#set_platformspeed
>
> Jaim
>
> > On 25 Jul 2017, at 20:23, Angel Herráez  wrote:
> >
> > I've just visited (first time)
> > http://dipc.ehu.es/bondslam/index.php/Hypervalence
> >
> > and I can see both molecule and  surface
> >
> > So either you just fixed it or there is some caching problem
> >
> >
> > ---
> > El software de antivirus Avast ha analizado este correo electrónico en
> busca de virus.
> > https://www.avast.com/antivirus
> >
> >
> > 
> --
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> 
> --
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
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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Re: [Jmol-users] Fwd: installing JSmol extension

[Robert Hanson]

right - well, you need to fix that  on your page, Henry. Right now you have
what I showed there.
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Re: [Jmol-users] Fwd: installing JSmol extension

[Robert Hanson]

http://dipc.ehu.es/bondslam/index.php/Images/b/b4/CH3F_mo10.cub.jvxl

does not exist.
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Re: [Jmol-users] png files created in jsmol

[Robert Hanson]

Q: What is the purpose of using pngCheck?


On Sat, Jul 22, 2017 at 5:52 AM, Angel Herráez  wrote:

> Hi João
>
> Even though the PNG files are not validated by pngcheck, they are rendered
> correctly by many programs.
>
> It should be easy to implement the setting of  'set imageState off'
> in the page source for the Sage project, and then the product of the Export
> menu would be compliant.
>
>
> ---
> El software de antivirus Avast ha analizado este correo electrónico en
> busca de virus.
> https://www.avast.com/antivirus
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
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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Re: [Jmol-users] NIST Webbook

[Robert Hanson]

Great. Congratulations to NIST, if you are listening...

On Fri, Jul 21, 2017 at 1:46 AM, Otis Rothenberger 
wrote:

> Bob may already know this. NIST WebBook has a spiffy new web page format.
> Some compound pages in the WebBook now have 2d and 3d SDF files with IR and
> other data in the files. The NIST on site 3d viewer is Jmol.
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.org
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> 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
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] Jmol 14.20.3 - minor fixes

[Robert Hanson]

Looking for the latest version? * Download Jmol-14.20.3-binary.zip (69.7
MB)
 *

Jmol.___JmolVersion="14.20.3" // 2017.07.20

bug fix: ROTATE should not stop spin if it does not initiate a spin
bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3
compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate
atoms
bug fix: MOL file reading where isotope is indicated in atom line and V item
bug fix: MOL reader fails for H1, D, T isotopes indicated as symbols along
with isotope difference


-- 
Robert M. Hanson
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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Re: [Jmol-users] JSModel demo control problem

[Robert Hanson]

that's what it was. I'll restart my release process and have a release
within the hour.

On Thu, Jul 20, 2017 at 8:59 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> OK, I'll look into why rotate does that. I think it's a blanket call from
> cmdRotate() [aka cmdSpin()] that is not distinguishing that this is not a
> spin request.
>
> On Thu, Jul 20, 2017 at 3:11 AM, Angel Herráez <angel.herr...@uah.es>
> wrote:
>
>>
>> I agree that reset should stop spinning, but not that rotate also does it
>>
>> Anyway, there are workarounds by checking the special _spinning variable
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> 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
> 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
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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Re: [Jmol-users] JSModel demo control problem

[Robert Hanson]

OK, I'll look into why rotate does that. I think it's a blanket call from
cmdRotate() [aka cmdSpin()] that is not distinguishing that this is not a
spin request.

On Thu, Jul 20, 2017 at 3:11 AM, Angel Herráez  wrote:

>
> I agree that reset should stop spinning, but not that rotate also does it
>
> Anyway, there are workarounds by checking the special _spinning variable
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> 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
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] JSModel demo control problem

[Robert Hanson]

I just tried jmol-14.1.6_2014.01.14, and it was the same there. rotate
stops spin. Ah, but

reset

does  not reset spin in the older version. I think that must have been
considered a bug -- that reset did not stop spinning.

I think you are stuck with this behavior. reset really should stop spinning.

Bob



On Wed, Jul 19, 2017 at 9:38 AM, Angel Herráez  wrote:

> It seems that "rotate" cancels the spin
>
> I have no clue if this has ever been by design.
>
> You could apply a fix by reading the spinning state before doing the
> rotate and reapplying it later:
>
> Jmol.jmolCheckbox(myJmol,
>   "reset;",
>   "ss = _spinning; reset; rotate x 90; if (ss) { spin on; }",
>   "Base-stacking");
>
>
> And why do you have in your spin checkbox those complex commands?
>
> Jmol.jmolCheckbox(myJmol, "spin off; spin on;", "spin on; spin off;",
> "Spin", true);
>
> I would just do
> Jmol.jmolCheckbox(myJmol, "spin on;", "spin off;", "Spin", true);
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
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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Re: [Jmol-users] loading gzipped files

[Robert Hanson]

That class was inadvertently left out of Jmol.jar and the JSmol site. Sorry
about that! Will do a release tonight, I hope.


On Wed, Jul 19, 2017 at 6:52 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> I'll look into the gzip problem.
> ​
>



-- 
Robert M. Hanson
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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Re: [Jmol-users] loading gzipped files

[Robert Hanson]

I'll look into the gzip problem.
​
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Re: [Jmol-users] Jmol 14.20.2 - replaces 14.20.1

[Robert Hanson]

Ah, I see it, too, now in IE 11. OK, I will look into that.



On Wed, Jul 12, 2017 at 1:40 PM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> Thanks Bob
>
>
>
> I haven’t been able to break the JSMol chirality finder using Chrome in a
> Windows 7 PC nor using
>
> Firefox 52.2 in Linux, in this version, in contrast to version 14.20.1, so
> we are another step
>
> forward.
>
>
>
> However it still fails as before in IE11 or in Firefox 22 in a PC.
>
> To avoid any possibility of cache trouble, I used two different other user
> ids and a public PC rather than
>
> my office one and my own id.
>
>
>
> The error message in Firefox is still
>
> RangeError:  arguments array passed to Function.prototype.apply is too
> large
>
>
>
> I was testing it on my P5S2Br molecule, but got the same error message on
> others of my website molecules,
>
> if they required the use of Rule 4b.
>
>
>
> Is it failing because these are older implementations of HTML5 and it is
> trying to use a newer feature?
>
>
>
> I suppose there might be a common university web cache which all of our
> machines are going through,
>
> and over which I have no control, but I do not know that.
>
>
>
>Bruce
>
>
>
> *From:* Robert Hanson [mailto:hans...@stolaf.edu]
> *Sent:* 10 July 2017 23:23
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* [Jmol-users] Jmol 14.20.2 - replaces 14.20.1
>
>
>
> Jmol.___JmolVersion="14.20.2" // 2017.07.09
>
> bug fix: CIPChirality adding presort for Rules 4a and 4c (test12.mol; 828
> lines)
> bug fix: write SDF and write MOL do not set atom parity field
> bug fix: JavaScript JSmol broken for chirality due to bug in
> Clazz.clone(obj)
>
> bug fix: Upgrade of natural abundance average masses (no significant
> changes here):
>
>   // all numbers except radionuclides from:
>   // Atomic weights of the elements 2013 (IUPAC Technical Report)
>   // Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul
> De Bièvre,
>   // Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss,
> Thomas Walczyk,
>   // Thomas Prohaska  Published Online: 2016-02-24 | DOI:
> https://doi.org/10.1515/pac-2015-0305
>   // https://www.degruyter.com/view/j/pac.2016.88.issue-3/
> pac-2015-0305/pac-2015-0305.xml
>
> /* 1 H */ 1.008f, 4.002f,
> /* 2 Li */ 6.9675f, 9.012f,  10.8135f, 12.0106f, 14.006f, 15.999f,
> 18.998f, 20.1797f,
> /* 3 Na */ 22.989f, 24.307f, 26.981f, 28.084f, 30.973f, 32.059f,
> 35.4515f, 39.948f,
> /* 4 K */ 39.0983f, 40.078f, 44.955f, 47.867f, 50.9415f, 51.9961f,
> 54.938f, 55.845f, 58.933f, 58.6934f, 63.546f, 65.38f, 69.723f, 72.63f,
> 74.921f, 78.971f, 79.904f, 83.798f,
> /* 5 Rb */ 85.4678f, 87.62f, 88.905f, 91.224f, 92.906f, 95.95f,
> 98.91f, 101.07f, 102.905f, 106.42f, 107.8682f, 112.414f, 114.818f, 118.71f,
> 121.76f, 127.6f, 126.904f, 131.293f,
> /* 6 Cs, Ba, actinides */132.905f, 137.327f, 138.905f, 140.116f,
> 140.907f, 144.242f, 144.9f,  150.36f, 151.964f, 157.25f, 158.925f, 162.5f,
> 164.93f, 167.259f, 168.934f, 173.054f, 174.9668f,
> /* 6 Hf */  178.49f,180.947f,183.84f,186.207f,190.23f,192.217f,195.
> 084f,196.966f,200.592f,204.3835f,207.2f,208.98f,210f, 210f, 222f,
> /* 7 Fr, Ra, lanthanides */ 223f, 226.03f, 227.03f, 232.0377f,
> 231.035f, 238.028f, 237.05f, 239.1f, 243.1f, 247.1f, 247.1f, 252.1f,
> 252.1f, 257.1f, 256.1f, 259.1f, 260.1f,
> /* 7 Rf - Mt */ 261f, 262f, 263f, 262f, 265f, 268f
>
>
>
>
> --
>
> Robert M. Hanson
> 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
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> 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
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] PubChem Load

[Robert Hanson]

There are several possible reasons for this: charge states, resonance
structures, etc. Possibly even different depositions, I'm not sure.
​
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[Jmol-users] Jmol 14.20.2 - replaces 14.20.1

[Robert Hanson]

Jmol.___JmolVersion="14.20.2" // 2017.07.09

bug fix: CIPChirality adding presort for Rules 4a and 4c (test12.mol; 828
lines)
bug fix: write SDF and write MOL do not set atom parity field
bug fix: JavaScript JSmol broken for chirality due to bug in
Clazz.clone(obj)

bug fix: Upgrade of natural abundance average masses (no significant
changes here):

  // all numbers except radionuclides from:
  // Atomic weights of the elements 2013 (IUPAC Technical Report)
  // Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul
De Bièvre,
  // Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss,
Thomas Walczyk,
  // Thomas Prohaska  Published Online: 2016-02-24 | DOI:
https://doi.org/10.1515/pac-2015-0305
  //
https://www.degruyter.com/view/j/pac.2016.88.issue-3/pac-2015-0305/pac-2015-0305.xml

/* 1 H */ 1.008f, 4.002f,
/* 2 Li */ 6.9675f, 9.012f,  10.8135f, 12.0106f, 14.006f, 15.999f,
18.998f, 20.1797f,
/* 3 Na */ 22.989f, 24.307f, 26.981f, 28.084f, 30.973f, 32.059f,
35.4515f, 39.948f,
/* 4 K */ 39.0983f, 40.078f, 44.955f, 47.867f, 50.9415f, 51.9961f,
54.938f, 55.845f, 58.933f, 58.6934f, 63.546f, 65.38f, 69.723f, 72.63f,
74.921f, 78.971f, 79.904f, 83.798f,
/* 5 Rb */ 85.4678f, 87.62f, 88.905f, 91.224f, 92.906f, 95.95f, 98.91f,
101.07f, 102.905f, 106.42f, 107.8682f, 112.414f, 114.818f, 118.71f,
121.76f, 127.6f, 126.904f, 131.293f,
/* 6 Cs, Ba, actinides */132.905f, 137.327f, 138.905f, 140.116f,
140.907f, 144.242f, 144.9f,  150.36f, 151.964f, 157.25f, 158.925f, 162.5f,
164.93f, 167.259f, 168.934f, 173.054f, 174.9668f,
/* 6 Hf */
178.49f,180.947f,183.84f,186.207f,190.23f,192.217f,195.084f,196.966f,200.592f,204.3835f,207.2f,208.98f,210f,
210f, 222f,
/* 7 Fr, Ra, lanthanides */ 223f, 226.03f, 227.03f, 232.0377f,
231.035f, 238.028f, 237.05f, 239.1f, 243.1f, 247.1f, 247.1f, 252.1f,
252.1f, 257.1f, 256.1f, 259.1f, 260.1f,
/* 7 Rf - Mt */ 261f, 262f, 263f, 262f, 265f, 268f




-- 
Robert M. Hanson
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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Re: [Jmol-users] Jmol 14.20.1

[Robert Hanson]

Hmm. One thing is that I messed up with the JavaScript version -- I am
getting different errors, but nonetheless there are issues. I'll do some
tests tomorrow and get back to you, Bruce. We really should not be having
browser issues at all. I certainly test extensively in Firefox and Chrome
and have seen no such errors.

Bob

On Fri, Jul 7, 2017 at 3:00 PM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> Thanks Bob
>
>
>
> The CIPChirality additional Rules feature now works in Jmol.jar and in
> the Jmol_S java applet in
>
> IE11 or in Firefox 22.0 in Windows 7 or in Firefox 52.2 in Linux.
>
>
>
> As before (version 14.18.1), it still works in the JSmol HTML5 applet in
> Chrome in Windows 7 or
>
> in Firefox 52.2 in Linux.
>
>
>
> However, it still does not work in the JSmol applet in IE11 nor in the
> JSmol applet in Firefox 22.0 in
>
> Windows 7.I have emptied the respective caches, and the JSmol version
> is shown as
>
> 14.20.1.
>
> The error message (in Firefox) is still, as before,
>
> RangeError:  arguments array passed to Function.prototype.apply is too
> large
>
> If one accepts this message twice, the Rule 1a chiralities only are shown,
> not the rule 4b chiralities,
>
> as was the case in version 14.18.1
>
>
>
> For a bigger molecule with some 4b chirality, JSmol also fails in Chrome
> or in Firefox in Linux, with a message
>
> script ERROR:  TypeError:  Cannot rad property ‘intValue’ of null
> J.shape.Labels
>
> set label
>
>
>
>   Bruce
>
>
>
> *From:* Robert Hanson [mailto:hans...@stolaf.edu]
> *Sent:* 07 July 2017 01:46
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* [Jmol-users] Jmol 14.20.1
>
>
>
> Download Jmol-14.20.1-binary.zip (69.7 MB)
> <https://sourceforge.net/projects/jmol/files/latest/download?source=files>
>
> Jmol.___JmolVersion="14.20.1"
>
> new feature: BZ2 compressed file reader
>   -- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
>   -- Apache license
>
> bug fix: ADF reader not accepting Xx.name atom ids
>
> bug fix: SMILES generator can show wrong @/@@ or stereochemical type for
> some allenes and cumulenes
>
> bug fix: CIPChirality additional Rules 1b, 4b, and 4c fixes (substituted
> cubanes; multiple branched branches; 841 lines)
>
>
>
> --
>
>
>
>
>
>
>
>
>
>
>
> *Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN
> http://www.stolaf.edu/people/hansonr <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*
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> 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
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] No atom picking with modifier keys

[Robert Hanson]

should be working  now -- check what I just released today. I was having
trouble because I missed this in my own documentation: * In the
explanations given below, it is presumed that we have set picking SELECT
GROUP*

On Thu, Jul 6, 2017 at 4:13 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de>
wrote:

> Am 06.07.17 um 16:26 schrieb Robert Hanson:
>
>> I'm not getting any of that to work. Are you?
>>
>> Yes, all five combinations work for me both in Jmol 14.18.1 Java and
> Javascript on MacOS 10.11.6 (El Capitan) in Safari 9.1.2 and Waterfox
> 53.0.3.
>
> Regards,
> Rolf
>
> On Wed, Jul 5, 2017 at 11:08 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de
>> <mailto:rolf.hue...@leibniz-fli.de>> wrote:
>>
>> Am 06.07.17 um 05:06 schrieb Robert Hanson:
>>
>> Rolf, what is the expected action of
>>
>> set pickingStyle select extendedSelect
>>
>> ?
>>
>> It is described in the scripting documentation:
>>
>> left-click  selects just that group, like rasmol;
>> shift-left-clicktoggles the group selected/not selected;
>> alt-left-click  appends the group to the current selection;
>> alt-shift-left-clickremoves the group from the current
>> selection;
>> left-click off modelexecutes (select none);
>>
>>
>> Regards,
>> Rolf
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> <mailto:Jmol-users@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> <https://lists.sourceforge.net/lists/listinfo/jmol-users>
>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> 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
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> ___
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>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
> 
> --
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>



-- 
Robert M. Hanson
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] Jmol 14.20.1

[Robert Hanson]

 Download Jmol-14.20.1-binary.zip (69.7 MB)


Jmol.___JmolVersion="14.20.1"

new feature: BZ2 compressed file reader
  -- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
  -- Apache license

bug fix: ADF reader not accepting Xx.name atom ids

bug fix: SMILES generator can show wrong @/@@ or stereochemical type for
some allenes and cumulenes

bug fix: CIPChirality additional Rules 1b, 4b, and 4c fixes (substituted
cubanes; multiple branched branches; 841 lines)



-- 












*Robert M. HansonProfessor of ChemistrySt. Olaf CollegeNorthfield,
MNhttp://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] No atom picking with modifier keys

[Robert Hanson]

I'm not getting any of that to work. Are you?

On Wed, Jul 5, 2017 at 11:08 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de>
wrote:

> Am 06.07.17 um 05:06 schrieb Robert Hanson:
>
>> Rolf, what is the expected action of
>>
>> set pickingStyle select extendedSelect
>>
>> ?
>>
> It is described in the scripting documentation:
>
> left-click  selects just that group, like rasmol;
> shift-left-clicktoggles the group selected/not selected;
> alt-left-click  appends the group to the current selection;
> alt-shift-left-clickremoves the group from the current
> selection;
> left-click off modelexecutes (select none);
>
>
> Regards,
> Rolf
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> 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
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] No atom picking with modifier keys

[Robert Hanson]

Rolf, what is the expected action of

set pickingStyle select extendedSelect

?

On Tue, Jul 4, 2017 at 8:29 AM, Rolf Huehne 
wrote:

> Hi Bob,
>
> I would like to implement my own atom pick mode, providing flexibility by
> using modifier keys like (SHIFT, ALT).
>
> In the standard mode, after the commands
> "set picking ATOM; set PickingStyle SELECT extendedSelect",
> atoms can be picked with one or more modifier keys pressed.
>
> But after the command "set picking on" and setting a callback with the
> command
> 'set pickCallback "jmolscript: pickAction()'
> the callback function 'pickAction' is only called in Jmol 14.18.1 if no
> modifier key is pressed.
>
> Q: Is this a bug or unfortunately the intended behaviour?
>
> Regards,
> Rolf
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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>



-- 
Robert M. Hanson
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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Re: [Jmol-users] SMARTS question

[Robert Hanson]

make sure you have loaded the file with

set pdbAddHydrogens

SMARTS is really not designed to work with models that do not indicate
bonding.

You  can also use Jmol BioSMARTS and target the sequences directly.




On Thu, Jun 29, 2017 at 12:28 PM, Eric Martz 
wrote:

> This selects the aromatic ring carbons of Phe and Tyr:
>
> rings6 = {*}.find("SMARTS","c1c1", true)
>
> It does not select the 6-atom ring of Trp.
>
> This selects the ring of His:
>
> ringsh = {*}.find("SMARTS","c1cncn1", true)
>
> How do I select the 5 and 6 atom rings of Trp?
>
> Thanks, Eric
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
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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Re: [Jmol-users] getting the applet ID

[Robert Hanson]

Well, if you wrote the page, you should know, right? ;)

All applets are registered in Jmol._applets.
​
Bob
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Re: [Jmol-users] Find/chemical

[Robert Hanson]

thanks, that is good to know.
​
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Re: [Jmol-users] Invert Stereochemistry

[Robert Hanson]

Probably not. But you can always use

select *
invertselected plane xy

for an enantiomer.

​Bob
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Re: [Jmol-users] Find/chemical

[Robert Hanson]

I don't believe you can set the timeout for an AJAX call in a browser. Can
you? If so, we're not doing that but probably should. It's probably 60
seconds. You can do that with PHP, I know...

Bob
​
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Re: [Jmol-users] nucleic acid representation in Jmol

[Robert Hanson]

On Tue, Jun 13, 2017 at 7:27 AM, Wayne Decatur via Jmol-users <
jmol-users@lists.sourceforge.net> wrote:

> Hi,
> Is `set backboneSteps` removed? I see `set cartoonSteps` now in use at the
> awesome http://jmol.x3dna.org.
>
>
Oooh, thank you, Wayne, for that shout-out. It was fabulously fun putting
that together. Really developed nicely, and I hear that the paper may be
featured on the cover of Nucleic Acids Research (
https://www.ncbi.nlm.nih.gov/pubmed/28472503)

Yes, in the development of that page, I realized that this feature had to
be a cartoon feature, not a backbone feature. Backbone has the oddness that
it only shows up if there are two adjacent residues. Cartoon is different
-- it can appear even if there is only one. This is what was happening. The
release note reads:

bug fix: backboneSteps moved to cartoonSteps
// order of checking for TRUE is:
// cartoonBlocks, cartoonBaseEdges, cartoonSteps, cartoonLadders,
cartoonRibose

JmolVersion="14.11.1" // 2017-04-03

bug fix: set cartoonBlocks; set cartoonBlockHeight x.x
 -- needs to be cartoon, not backbone (needs to be single-monomer based)
 -- replaces set backboneBlocks; set backboneBlockHeight x.x from 14.11.0
 -- for nucleic only
 -- overrides set cartoonSteps and cartoonBaseEdges
 -- uses DSSR data if present (using calculate structure DSSR or load
=/dssr)
 -- displays a DSSR block for each base based on dssr.nts.frame
 -- x.x is height of box in Angstroms (default 0.5)





> In the Jmol documentation, `set backboneSteps` is still shown as part of a
> demo script under '[atom expressions]' at https://chemapps.stolaf.
> edu/jmol/docs/#atomexpressions  for 'WITHIN(DSSR,type)'
> '
>
>
I wll get that fixed.


> Is there anyway to use `ribbon` for nucleic acid and have the cartoonSteps
> shown between the ribbon but without other parts of the cartoon being
> visible, i.e., the backbone?
>

I don't think so. I get your point, though, that if it were backbone you
could do that. Do you see that as an important feature?

Bob
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Re: [Jmol-users] cloning part of a model into another frame

[Robert Hanson]

You might not get all the information in a PDB file, but I think you could
select the atoms and append them:

load =1blu
select sf4
x = write("PDB")
load append inline @x

​
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

I think it gets back to the issue of what is embedded in what. The magic of
the Jmol applet, of course, is that you can embed it in whatever context
you want -- Jena3D, for example. This is not directly possible for the Jmol
application. (It can be done, but you have to be a Java programmer to do
it.) So I am not seeing a solution for people who want to embed the Jmol
applet in a larger context. JavaFX is the other way around -- embed a web
page in a devoted Java project.

Bob

​
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Re: [Jmol-users] display of contacts in two frames/models

[Robert Hanson]

Not a bug. You just have to be careful to use the ID and atom selection
carefully

load =1blu
contact ID c1 {SF4}
load append =1d66
contact ID c2 {nucleic and 2.1}

If you leave off ID, then the two have the same default id, "contact1", and
so the first is lost when the second appears.
If you leave off "and 2.1", then you risk picking up contacts between the
two models or within the first.



On Sat, Jun 10, 2017 at 10:06 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> definitely a bug.
>



-- 
Robert M. Hanson
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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Re: [Jmol-users] display of contacts in two frames/models

[Robert Hanson]

definitely a bug.
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

I don't know anything about JavaFX, but it's not clear to me there has
>> been any development on it since 2012 or 2014. Maybe just an idea that
>> never took off? Do you see some advantage to this?
>>
>> Since I don't have done any Java programming I will know even less. When
> I spoke to a computer scientist about the problem of dropped NPAPI plugin
> support by an increasing number of browsers, he suggested to become
> independent of any browser by combining the applet with already existing
> Java HTML5/CSS/Javascript engines. I have chosen the example engines just
> to illustrate the idea, not because I know anything particular about their
> suitability.
>
> It seems that Oracle still recommends JavaFX for Desktop applications.
> At last that is what the following post about the future of JavaFX from
> 2016 (unfortunately in German) suggests: https://jaxenter.de/hart-aber-
> fair-welche-zukunft-hat-javafx-37199 . Among other things it describes
> the reaction of Oracle to a request of an interest group of german Java
> users (iJUG) about the future of JavaFX. According to this Oracle
> recommends it and has an official roadmap for it until 2028.
>
> The advantage I see with the general idea is that each Jmol-based web
> service, running in the future with the Javascript version, could also be
> run as a Java desktop application.
>
>
I think we're one level off here. You can always run Jmol.jar if you want
Jmol's desktop application, and nothing is going to change about that. It
isn't an applet, so there is no browser issue.

My quick read of the JavaFX tutorial [
docs.oracle.com/javafx/2/overview/jfxpub-overview.htm] suggests that it is
simply a newer way to build an independent Java desktop application like
Jmol.jar, but it has a wider set of user interface capability than what we
use now (Swing). Thus, they talk about being able to insert a full-fledged
webkit browser into the application, to use CSS for styling, to dynamically
create a user interface -- that sort of thing.

And although the general Javascript performance is catching up with Java,
> my observation is that it the performance is less stable. This means that a
> task for example took anything from 60 seconds to 120 seconds (or even
> more) in the Javascript version, depending on how the browser 'felt'. In
> contrast the Java version stably needed about ten seconds, run on the same
> system before and after the Javascript version.
>
> Yes. By "felt" you mean that the browser will manage its threads relating
to tabs and other dyanamic content (e.g. ads), and it may shift a running
JavaScript app to a lower priority more likely than a running Java
application would or, in particular, then a running Java applet would.

A 1:12 performance ratio seems on the outside of what I have observed, but
I am sure that can happen. We are seeing 1:3 to 1:6 commonly.

I'm pretty sure the real benefit would be to use the WebGL option in JSmol,
or at least to develop that further. For example, by merging NGL's
excellent 3D capabilities into JSmol.

Rolf, do you have a sense of whether these slow-downs are rendering issues?
Or do they happen in relation to file opening, model construction, or
surface construction?

Bob



>
> Regards,
> Rolf
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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-- 
Robert M. Hanson
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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Re: [Jmol-users] Jmol SMILES Question

[Robert Hanson]

*print {*}.find("smiles/nostereo")*
see https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0160-4


*Directives /noStereo/ and /invertStereo/ are very useful because they
allow re-use of SMILES strings for different types of stereochemical
matches without having to remove or switch the stereochemical designations
in the strings themselves, which can be quite complicated. The directive
/noStereo/ simply ignores all stereochemistry indicated in the SMILES
string, including both stereochemistry at chirality centers as well as
cis/trans double-bond stereochemistry. The directive /invertStereo/ inverts
all chirality designations, allowing efficient checking for enantiomers. *
Bob

On Thu, Jun 8, 2017 at 3:41 PM, Otis Rothenberger 
wrote:

> Bob,
>
> Can Jmol generate a non-stereo SMILES for a chiral model in the window?
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>


-- 
Robert M. Hanson
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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Re: [Jmol-users] Jmol 14.18.1

[Robert Hanson]

I confirm that Jmol.jar is broken for generation of Cahn-Ingold-Prelog
stereochemical descriptors in Java; the JavaScript should be OK.

On Thu, Jun 8, 2017 at 12:55 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> OK, it could be that I messed up with the distribution. That can happen if
> I forget to do a thorough cleaning of the directories, which is the case
> this time.
> ​
> Bob
>
>


-- 
Robert M. Hanson
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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Re: [Jmol-users] Jmol 14.18.1

[Robert Hanson]

OK, it could be that I messed up with the distribution. That can happen if
I forget to do a thorough cleaning of the directories, which is the case
this time.
​
Bob
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

On Thu, Jun 8, 2017 at 10:58 AM, Rolf Huehne <rolf.hue...@leibniz-fli.de>
wrote:

> Am 08.06.17 um 14:41 schrieb Robert Hanson:
>
>> RIP,  Java applets.
>>
>> Since there still are many situations where the superior Java performance
> would be helpful (large structures; surfaces; complex Jmol scripts that are
> running about 50 times slower in the Javascript version) it would still be
> good to have a Java version with the flexibility of the applet to build
> customized user interfaces.
>
> sorry, didn't mean to imply that we were dropping applet production.  It's
all produced in a few clicks of a button -- Jmol app, Jmol applet,
JmolData, JSmol. So I will keep that happening the same.



> I am wondering how much effort it would be to extend the applet by a
> HTML/CSS rendering and Javascript engine like it is provided by systems
> like 'JavaFX - WebView Component (https://docs.oracle.com/javas
> e/8/javafx/api/toc.htm https://stackoverflow.com/ques
> tions/2438201/pure-java-html-viewer-renderer-for-use-in-a-scrollable-pane),
> Oracle Nashorn (http://www.oracle.com/technetwork/articles/java/jf14-
> nashorn-2126515.html), and HtmlUnit (http://htmlunit.sourceforge.net/).
>
> I woud guess one of the critical points would be how much of the
> Javascript/Applet communication would still be possible in such application.
>

I don't know anything about JavaFX, but it's not clear to me there has been
any development on it since 2012 or 2014. Maybe just an idea that never
took off? Do you see some advantage to this?

Bob
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

09/29/2005  08:18 AM 1,813,012 ch3cl-density.cub
09/17/2006  07:47 AM   600,830 ch3cl-density.cub.gz
06/08/2017  08:39 AM 4,631 ch3cl-density.jvxl
06/08/2017  08:40 AM 2,928 ch3cl-density.jvxl.gz

So that is 390:1 with just the JVXL, or 619:1 compression using JVXL+GZ.

(There is never a need to use GZ for web-based files; they almost certainly
will be automatically gzipped by the server anyway.)

So I can't say I'm super impressed. If it's truly full volume data, that
would be impressive.

Bob


On Thu, Jun 8, 2017 at 7:48 AM, Rzepa, Henry S <h.rz...@imperial.ac.uk>
wrote:

>
> > On 8 Jun 2017, at 13:45, Robert Hanson <hans...@stolaf.edu> wrote:
> >
> > ps -- neither of the VMD images at http://www.ch.imperial.ac.uk/
> rzepa/blog/?p=18365#comment-243964 are volume rendering, by the way. They
> are just surfaces, one with reflection; one just a mesh. Right?
>
> Yes.  The  reduction in cube size of  ~500 is impressive, but then  JVXL
> manages ~100 (and perhaps more if compressed?)
>
> Contact  Brian Skinner for the inside story.  bsk...@alum.mit.edu
>
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

ps -- neither of the VMD images at
http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 are volume
rendering, by the way. They are just surfaces, one with reflection; one
just a mesh. Right?

On Thu, Jun 8, 2017 at 7:41 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> RIP,  Java applets.
>
> On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S <h.rz...@imperial.ac.uk>
> wrote:
>
>> I have had a look at Safari preview 32.  In the preferences/security tab,
>> the current production safari has settings for
>>
>> 1. Allow WebGL
>> 2. Allow Internet Plugins,  and in this latter one can configure to
>> allow  Java.
>>
>> In Safari 32, both of these are now gone.   With  High Sierra developer
>> preview about to be released into  beta, may bring confirmation that
>> Safari too has now not merely been deprecated but disallowed.
>>
>> If correct, this means that Jmol.jar can only now run in application
>> mode, and not as a browser plugin.
>>
>> Still,  Apple promise that the new Safari will be  “faster”, although  I
>> suspect it has some way to go to be as fast as compiled Java.
>>
>>
>> I wonder what the missing  WebGL means? It never really took off did it!
>>
>
> ?? WebGL is fantastic. Everyone is using it, including JSmol if you use
> that option. See this note relative to WebGPU, though:
> https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/
>
> Is curious, though. I can't seem to find any reference to WebGL at the
> preview site. Where do you see that, Henry?
>
>
> Bob
>
>


-- 
Robert M. Hanson
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Robert Hanson]

RIP,  Java applets.

On Thu, Jun 8, 2017 at 5:29 AM, Rzepa, Henry S 
wrote:

> I have had a look at Safari preview 32.  In the preferences/security tab,
> the current production safari has settings for
>
> 1. Allow WebGL
> 2. Allow Internet Plugins,  and in this latter one can configure to allow
> Java.
>
> In Safari 32, both of these are now gone.   With  High Sierra developer
> preview about to be released into  beta, may bring confirmation that
> Safari too has now not merely been deprecated but disallowed.
>
> If correct, this means that Jmol.jar can only now run in application mode,
> and not as a browser plugin.
>
> Still,  Apple promise that the new Safari will be  “faster”, although  I
> suspect it has some way to go to be as fast as compiled Java.
>
>
> I wonder what the missing  WebGL means? It never really took off did it!
>

?? WebGL is fantastic. Everyone is using it, including JSmol if you use
that option. See this note relative to WebGPU, though:
https://webkit.org/blog/7380/next-generation-3d-graphics-on-the-web/

Is curious, though. I can't seem to find any reference to WebGL at the
preview site. Where do you see that, Henry?


Bob
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Re: [Jmol-users] HDF5 compression for Cube files?

[Robert Hanson]

Henry,

Good to hear from you!

Could be interesting. From my reading, HDF5 just uses standard ZLIB
compression  (ZIP, GZ) [
https://support.hdfgroup.org/HDF5/faq/compression.html]. I suppose there
might be some difference with that and its alternative SZIP, but I don't
find any comparisons for that with a quick search.

>From the blog comment, it looks to me he is talking specifically about
volume rendering, which is not what JVXL is for, and which Jmol is not set
up to do. JVXL is specifically for surface rendering, where it reduces a 3D
data problem to a 1D problem, thus the huge 300+:1 efficiencies relate to
cube files.

Bob




On Thu, Jun 8, 2017 at 12:28 AM, Rzepa, Henry S 
wrote:

> I have used the excellent  JVXL for reducing cube files to a selected
> isosurface.  Brian Skinner
>
> ( http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 ) has
> indicated work he is doing o the  HDF5 format for reducing cube files,
> where he can obtain up to 530 fold reduction in file sizes.
>
> Does anyone know if  HDF5 has been investigated for  JSmol support?
>
>
> Henry Rzepa, http://orcid.org/-0002-8635-8390
>
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
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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Re: [Jmol-users] Jmol 14.18.1

[Robert Hanson]

You will have to clear your cache.

On Wed, Jun 7, 2017 at 11:43 AM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> Sorry Bob, but this version fails to do any chirality labelling for me,
> for either of my two models which you
>
> looked at yesterday.
>
> The following is copied from the Jmol Script Console:
>
>
>
> label %[chirality]
>
>
>
> script ERROR: java.lang.AbstractMethodError: org.jmol.modelset.Atom.
> getEdges()[Lorg/jmol/util/SimpleEdge; org.jmol.shape.Labels set label
>
>
>
> Bruce
>
>
>
> *From:* Robert Hanson [mailto:hans...@stolaf.edu]
> *Sent:* 07 June 2017 14:15
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* [Jmol-users] Jmol 14.18.1
>
>
>
> Jmol.___JmolVersion="14.18.1"  // 2017.06.06
>
> *Jmol-14.18.1-binary.zip (69.8 MB)
> <https://sourceforge.net/projects/jmol/files/latest/download?source=files>*
>
> new feature: WRITE SDF writes > < user data
>  -- can be set using   MODEL PROPERTY "molData" x  where x is an
> associative array
>  -- can be read using _M.molData
>
> new feature: associativeArray.pop() -- clears associativeArray
>
> new feature: assArray1.push(assArray2) -- adds all key/value entries in
> assArray2 to assArray1.
>
> new feature: assArray1 + assArray2  -- adds all key/value entries into a
> new associative array. (Complements a1 - a2)
>
> bug fix: CIP misses Rule 4b cases where a branching atom has R or S
> chirality.
>  -- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
>  -- see AY236.179 (3D structure was diasteriomer, so I missed that)
>
> bug fix: WRITE MOL should not generate >  because it
> is  not SDF format
> bug fix: WRITE SDF should generate >  with a
> trailing space
>
> bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
> .[C@H]2 (new group and attached to a connection number)
> bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
>
>
>
>
>
> --
>
> Robert M. Hanson
> 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
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> 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
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] Jmol 14.18.1

[Robert Hanson]

Jmol.___JmolVersion="14.18.1"  // 2017.06.06

*Jmol-14.18.1-binary.zip (69.8 MB)
*

new feature: WRITE SDF writes > < user data
 -- can be set using   MODEL PROPERTY "molData" x  where x is an
associative array
 -- can be read using _M.molData

new feature: associativeArray.pop() -- clears associativeArray

new feature: assArray1.push(assArray2) -- adds all key/value entries in
assArray2 to assArray1.

new feature: assArray1 + assArray2  -- adds all key/value entries into a
new associative array. (Complements a1 - a2)

bug fix: CIP misses Rule 4b cases where a branching atom has R or S
chirality.
 -- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
 -- see AY236.179 (3D structure was diasteriomer, so I missed that)

bug fix: WRITE MOL should not generate >  because it
is  not SDF format
bug fix: WRITE SDF should generate >  with a trailing
space

bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4





-- 
Robert M. Hanson
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] Jmol 14.7.2

[Robert Hanson]

minor bug fixes.

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.17/Jmol%2014.17.2/

JmolVersion="14.17.2" // 2017.06.03

bug fix: WRITE FILE not working when file has been cached.
bug fix: array.find("regex...","") does not reset RegExp each time it runs
RegExp.exec() so does not find all possibilities (Rolf)

code: CIPChirality.java fully interfaced using SimpleNode and SimpleEdge



-- 
Robert M. Hanson
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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Re: [Jmol-users] using mutate on the first model with 2 loaded files

[Robert Hanson]

Right, Angel. The morphing business requires creating new atoms, and that
currently cannot be done for any but the last model. I know it is not
ideal, but there are just too many dependencies on atom index to find them
all and make sure they are all updated correctly if atoms are added at
other model boundaries.

On Sun, Jun 4, 2017 at 7:19 AM, Angel Herráez  wrote:

> Hi Bob
>
> Any chance that I can use "mutate" on a first model when I have loaded two
> models (2 files into 2 frames)?
> I am testing the different syntaxes from the documentation but it seems
> impossible. Some sections do mention "in the last model".
>
> Can you please confirm?
>
> Thanks
>
>
> ---
> El software de antivirus Avast ha analizado este correo electrónico en
> busca de virus.
> https://www.avast.com/antivirus
>
>


-- 
Robert M. Hanson
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] Jmol 14.17.1

[Robert Hanson]

*Jmol-14.17.1-binary.zip (69.8 MB)
*
Jmol.___JmolVersion="14.17.1"  // 2017.05.27

new feature: atom property x.cipRule
 -- CIP sequence rule deciding this center
 -- one of 1a, 1b, 2, 3, 4a, 4b, 4c, 5, or blank

bug fix: polyhedra broken in Jmol 14.10.0

bug fix: finalizing CIP algorithm
 -- adding spiro chirality from P-93.5.3
 -- completing root path for auxiliary descriptors

bug fix: JSmol: JSME/JSmol 2D->3D fails when one H of a CH2 is explicitly
wedge and the other H is implicit (not shown at all). (JSmolJME.js)

code:

/**
 * A fully validated relatively efficient implementation of
Cahn-Ingold-Prelog
 * rules for assigning R/S, M/P, and E/Z stereochemical descriptors. Based
on
 * IUPAC Blue Book rules of 2013.
 * https://iupac.org/projects/project-details/?project_nr=2001-043-1-800
 *
 * Features include:
 *
 *  - deeply validated
 *
 *  - implemented in Java (Jmol) and JavaScript (JSmol)
 *
 *  - only two Java classes; roughly 1000 lines
 *
 *  - efficient, one-pass process for each center using a single finite
digraph for all auxiliary descriptors
 *
 *  - exhaustive processing of all 8 sequence rules (1a, 1b, 2, 3, 4a, 4b,
4c, 5)
 *
 *  - includes R/S, r/s, M/P (axial, not planar), E/Z
 *
 *  - covers any-length odd and even cumulenes
 *
 *  - uses Jmol conformational SMARTS to detect atropisomers and helicenes
 *
 *  - covers chiral phosphorus and sulfur, including trigonal pyramidal and
tetrahedral
 *
 *  - properly treats complex combinations of R/S, M/P, and seqCis/seqTrans
centers (Rule 4b)
 *
 *  - properly treats neutral-species resonance structures using fractional
atomic mass and a modified Rule 1b
 *
 *  - implements CIP spiro rule (BB P-93.5.3.1)
 *
 *  - detects small rings (fewer than 8 members) and removes E/Z
specifications for such
 *
 *  - detects chiral bridgehead nitrogens
 *
 *  - reports atom descriptor along with the rule that ultimately decided it
 *
 * Primary 236-compound Chapter-9 validation set (AY-236) provided by Andres
 * Yerin, ACD/Labs (Moscow).
 *
 * Mikko Vainio also supplied a 64-compound testing suite (MV-64), which is
 * available on SourceForge in the Jmol-datafiles directory.
 * (https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip).
 *
 * Additional test structures provided by John Mayfield.
 *
 * Additional thanks to the IUPAC Blue Book Revision project, specifically
 * Karl-Heinz Hellwich for alerting me to the errata page for the 2013 IUPAC
 * specs (http://www.chem.qmul.ac.uk/iupac/bibliog/BBerrors.html), Gerry
Moss
 * for discussions, Andres Yerin for discussion and digraph checking.
 *
 * Many thanks to the members of the BlueObelisk-Discuss group, particularly
 * Mikko Vainio, John Mayfield (aka John May), Wolf Ihlenfeldt, and Egon
Willighagen, for
 * encouragement, examples, serious skepticism, and extremely helpful
advice.
 *


-- 
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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Re: [Jmol-users] Old Question

[Robert Hanson]

Otis, you suggest:

*var molf2 = "' + molf1 + '"; load "@molf2";*

That's a fine way to do it. The LOAD command looks for "@..." and does that
special case conversion. An alternative load command is:

LOAD VAR molf2

or

LOAD VAR "mol2"

Bob


On Wed, May 24, 2017 at 9:09 PM, Otis Rothenberger 
wrote:

> Bob,
>
> This goes back almost a year to an JmolScript @ question. You resolved my
> @ problem in a detailed reply.
>
> Reviewing this old note, another question comes up. I do the following all
> the time:
>
> var molf2 = "' + molf1 + '"; load "@molf2";
>
> molf1 is a molfile string. Does this fall into the category of NOT best
> practice with @?
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
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>


-- 
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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Re: [Jmol-users] How does Jmol know the \alpha-helix and \beta-sheet

[Robert Hanson]

On Mon, May 22, 2017 at 9:08 AM, Angel Herráez  wrote:

> Hello, Huan
>
> Jmol uses 2 methods:
>
> 1st
> if the pdb file contains HELIX and SHEET records, Jmol uses those.
>
> 2nd
> if that is not the case, Jmol will calculate secondary structures using the
> DSSP algorithm
>
>
technically, DSSP 2.0, though it has the option to drop back to DSSP 1.0
using:

*calculate structure DSSP 1.0*

There are only subtle differences between these two versions of DSSP.

Bob
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[Jmol-users] Jmol 14.16.1

[Robert Hanson]

* Jmol-14.16.1-binary.zip (69.8 MB)

*Just
two items here -

- new load command option for ChEBI. These structures are all 2D drawings
(hashes and wedges), but they can be loaded with automatic 2D->3D
conversion.

- Cahn-Ingold-Prelog stereochemistry determination adds axial helicene M/P
chirality

Jmol.___JmolVersion="14.16.1" // 2017.05.19

new feature: load =chebi/nnchEBI 2D molecule load, with minimal
100-step minimization

bug fix: CML reader does not read 2D wedge/hash information

bug fix: CIP fix for missing branch descriptors; 984 lines

bug fix: CIP adds helicene M/P chirality
  - validated using CCDC structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF
  - http://pubs.rsc.org/en/content/articlehtml/2017/CP/C6CP07552E

code: CIP: additional simplification;
code: CIP status: implementation complete, including:
 All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5
 R/S, E/Z, M/P (odd-cumulene and helicene), r/s, seqCis/seqTrans
(as Z/E)
 fused benzenoid aromatic Mancude ring "Kekule weighted" atom
number adjustments



-- 
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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Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

[Robert Hanson]

I note that one could connect JSmol to any of these with only a little
work. Just hasn't been done.

On Mon, May 15, 2017 at 1:33 PM, Paul PILLOT <paulpil...@gmail.com> wrote:

> Dear Jmolers,
> the original message of this thread was posted one year and a half ago…
> and discussed about libraries using WebGL to display macromolecules.
>
> Since then, the landscape of webGL molecular viewers has reshaped:
> - PV is now in maintenance mode : "This project is currently in
> maintenance mode. I simply just don't have the time to work on it anymore.
> I'm happy to fix smaller bugs and answer support requests, though it might
> take a while until I can answer those. » from github repo
> <https://github.com/biasmv/pv>
>
> - chemDoodle webcomponents has not been updated since nov 2015
>
> - 3dmol.js and NGL (see original post below) are still actively developed
> and from the activity on their respective github accounts are gaining
> contributors and tractions
>
> - Litemol is another opensource viewer (written in typescript) :
> https://webchemdev.ncbr.muni.cz/LiteMol/
> it’s used by PDBe. The githug repo is here
> <https://github.com/dsehnal/LiteMol>
>
> - Molmil, is another open source viewer, used by PDBj. Demo here
> <http://gjbekker.github.io/molmil/> and github repo here
> <https://github.com/gjbekker/molmil>
> Article for reference : https://jcheminf.springeropen.com/articles/10.
> 1186/s13321-016-0155-1
> It uses a subset of Pymol’s command language
>
> -Paul
>
> Le 03-11-2015 à 16:05, Robert Hanson <hans...@stolaf.edu> a écrit :
>
> And don't forget that Jmol has a WebGL option, but I don't claim that it
> is any better than the others. It's not our forte, and it comes with a
> significant overhead if all you want is a molecule to show.
>
> On Tue, Nov 3, 2015 at 1:57 PM, Paul PILLOT <paulpil...@gmail.com> wrote:
>
>> Hi Angel,
>> feel free to include this comparison in the wiki for further reference.
>>
>> I fully agree with all your comments. Persistency of web libraries is an
>> important aspect.
>> Some are funded projects (3Dmol.js relies on a grant), some are academic
>> or backed by
>> public institutions. Open source development (such as public source
>> repositories) provide
>> an opportunity for future developments.
>> The ease of implementation of the library should also be taken into
>> account, especially if
>> you’re going for a multiple alternatives option.
>>
>> Vive Jmol !
>>
>>
>> > Le 03-11-2015 à 04:45, Angel Herráez <angel.herr...@uah.es> a écrit :
>> >
>> > Hi Paul
>> >
>> > Thank you for the information, it is very interesting. I had already
>> seen PV in
>> > action, but not others. I wonder how much hard work is being duplicated
>> in
>> > parallel.
>> >
>> > I'm quite sure that the better performance is due to WebGL, not to the
>> > efficiency of the software code.
>> >
>> > The old problem with WebGL was lack of support in old machines (graphic
>> > cards). I guess this is a nearly negligible worry today --though I
>> wonder about
>> > tablets.
>> >
>> > Another big issue is permanence; many programs are "experiments" that
>> > quickly go dead. I have not experienced this with 3D, but It happened
>> with
>> > 2D molecule drawing, very nice and promising ones stopped being
>> > developed. See http://biomodel.uah.es/en/DIY/
>> > http://biomodel.uah.es/en/DIY/comparison.htm
>> >
>> > That is worrisome when trying to choose.
>> >
>> > But anyway your comparison is very useful and one could design pages
>> > offerring altenatives to users, as e.g. RCSB is now doing: PV / JSmol /
>> > JmolJava
>> >
>> > If you don't mind, I'd be happy to add your comparison table to the Jmol
>> > Wiki, so we can easily find it and keep if updated.
>> >
>> > And finally, I wish some of the "expertise" of these programs would
>> entice
>> > someone to step ahead and grab the task of further implementing WebGL in
>> > Jmol (I'm not saying Bob Hanson)
>> >
>> > Long live Jmol!
>> >
>> >
>>
> Original post :
> Dear Jmolers,
> with the end of Java embedded plugins, we are now relying on JSmol for
> displaying molecular structures in web pages.
> If JSmol bio/geo/chemicabilities appear to me as limitless, I am
> encountering other limitations in respect with its performances : some web
> applications I made are particularly slow 

Re: [Jmol-users] labeling residue by position relative to observer

[Robert Hanson]

"sz" stands for "screen z"; smaller is closer.

select on sz = @{all.sz.min}

highlights closest atom

(sorry,  Eric!)

​Bob
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[Jmol-users] JmolVersion="14.15.3" // 2017-05-08

[Robert Hanson]

 * Download Jmol-14.15.3-binary.zip (69.8 MB)
 *
JmolVersion="14.15.3" // 2017-05-08

bug fix: SMARTS search for atropisomeric bond that is in an alicyclic ring
fails (Fred Ziegler)
  - used for M/P chirality check
  - for example:
   load $c1cc2c3-c4c5CC2.c5ccc4C.c3(C)c1
   select on smarts("a-a")
   calculate chirality
   print {*}.chirality.join("")

MM

bug fix: use of the less preferred name of Jmol token that has two optional
 forms ("fix" vs "fixed") as a VAR does not assign that variable
name
bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
bug fix: JVXL reader not reading Gaussian files with "1" in the third line,
5th field
bug fix: CIP M/P chirality
  test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
bug fix: CIP chirality nearly fully validated on ACD/Labs AY-236 set, with
some unimplemented aspects:

var skip = ({27 229}) || // E/Z only; missing chirality
   ({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) ||
// trigonal planar, square planar, or hypervalent
   ({32 33})  || // helicene
   ({201 202})|| // spirocyclic central (redundant) atom
designation missing (axial designation option)
   ({212 213})|| // chiral conformation 1,4-benzene in a ring
   ({38 84})  || // ignore -- 38: Mancude for cyclopentadienyl; 84:
unknown error with P compound
   ({203})|| // // chiral bridgehead amine

Issue: Full implementation of the rules requires a slight modification of
Rule 1b.
Specifically, aromatic duplicate atoms must reference the sphere of their
own parent, not their
duplicated atom.

 Three structures appear to be in error in the IUPAC Blue Book 2013.

,"147":"r,,,Rr,,,S" // r,,,Rr,,,R chiral phosphine -- I think Jmol
is right; disagrees with BB P-93.5.1.1.2 for S vs R
,"227":"SrSEErS" // S,,,r,S,,,E,,r,r  //  -- I think Jmol is right;
disagrees with BB P-93.5.7.2 for S vs. r
,"230":"@2D RrRsR" // r,,,Rs,,,R // p 1282   -- I believe Jmol is
correct, disagrees with BB P-93.6

 One structure awaiting full implementation of Rule 4b across all chirality
types, R/S, M/P, and seqCis/seqTrans

 ,"170":"Spp" // Jmol is missing the S -- mix of R/S and M/P for Rule 4b

 - 939 lines




-- 
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] Latest Jmol paper

[Robert Hanson]

Hot off the presses...

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365



*DSSR-enhanced visualization of nucleic acid structures in Jmol*

*Abstract*
Sophisticated and interactive visualizations are essential for making sense
of the intricate 3D structures of macromolecules. For proteins, secondary
structural components are routinely featured in molecular graphics
visualizations. However, the field of RNA structural bioinformatics is
still lagging behind; for example, current molecular graphics tools lack
built-in support even for base pairs, double helices, or hairpin loops.
DSSR (Dissecting the Spatial Structure of RNA) is an integrated and
automated command-line tool for the analysis and annotation of RNA tertiary
structures. It calculates a comprehensive and unique set of features for
characterizing RNA, as well as DNA structures. Jmol is a widely used,
open-source Java viewer for 3D structures, with a powerful scripting
language. JSmol, its reincarnation based on native JavaScript, has a
predominant position in the post Java-applet era for web-based
visualization of molecular structures. The DSSR-Jmol integration presented
here makes salient features of DSSR readily accessible, either via the
Java-based Jmol application itself, or its HTML5-based equivalent, JSmol.
The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format)
initiated from a Jmol or JSmol session and returns DSSR-derived structural
features in JSON format. This seamless combination of DSSR and Jmol/JSmol
brings the molecular graphics of 3D RNA structures to a similar level as
that for proteins, and enables a much deeper analysis of structural
characteristics. It fills a gap in RNA structural bioinformatics, and is
freely accessible (via the Jmol application or the JSmol-based website
http://jmol.x3dna.org).



-- 
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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Re: [Jmol-users] R: Jmol 14.15.2 -- chirality work complete: exception?

[Robert Hanson]

ps -- if you issue for that second sample:

MINIMIZE

(maybe twice? Don't know; I did that.) Then it works:

print {chirality != ""}.label("%a%[chirality]").join(",").replace("C","")

1Z,2Z,3E,4E,5Z,6Z,7Z,8Z,9Z,10Z

(carbon numbering, not naming)






On Fri, May 5, 2017 at 3:57 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Pino,
>
> The first structure shows no designations because designations are
> specifically removed for all ring sizes less than 8, and you have
> 7-membered rings there.
>
> In the second case, you have highly twisted double bonds, so the cis/trans
> determination cannot be made. They have to be planar.
> ​
>



-- 
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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Re: [Jmol-users] R: Jmol 14.15.2 -- chirality work complete: exception?

[Robert Hanson]

Pino,

The first structure shows no designations because designations are
specifically removed for all ring sizes less than 8, and you have
7-membered rings there.

In the second case, you have highly twisted double bonds, so the cis/trans
determination cannot be made. They have to be planar.
​
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[Jmol-users] Jmol 14.15.2 -- chirality work complete

[Robert Hanson]

Jmol 14.15.2 https://sourceforge.net/projects/jmol/files

fully implements all IUPAC 2013 Blue Book (
http://pubs.rsc.org/en/content/ebook/9780854041824) involved in:

   -- simple R/S and E/Z, with small-ring removal of E/Z
   -- odd and even cumulenes (E/Z, M/P)
   -- atropisomers (M/P)
   -- pseudochiral r/s and m/p
   -- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
   -- imine and diazine E/Z chirality

(In case "M/P" is new to you,  M(inus) and P(lus) are the preferred
designations now for axial and planar chirality rather than Ra and Sa,
respectively. I like this a lot, because it is simply the sign of the
associated torsion angle.)

Jmol does not implement hypervalent chirality (trigonal bipyramidal,
octahedral)

Bob

-- 
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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Re: [Jmol-users] ivxl

[Robert Hanson]

Fred,

I had no problems with this in just-released 14.15.2:

$ isosurface ch3cl-density.cub.gz map ch3cl-esp.cub.gz
$ write isosurface t.jvxl

reading isosurface data from c:/jmol-dev/bobtest/ch3cl-density.cub.gz
reading isosurface data from c:/jmol-dev/bobtest/ch3cl-esp.cub.gz
isosurface1 created  with cutoff=0.02 min=0.0 max=1.35334; isosurface
count: 1
isosurface full data range -0.007748252 to 10.191908 with color scheme
spanning -0.007748252 to 10.191908
1 id:isosurface1; model:0.0; vertices:1982; polygons:3960; visible:true;
dataRange:[-0.007748252, 10.191908, -0.007748252, 10.191908];
title:isosurface ch3cl-density.cub.gz map ch3cl-esp.cub.gz;




OK XJVXL 7884 c:/jmol-dev/bobtest/t.jvxl
$ zap
$ isosurface t.jvxl
reading isosurface data from c:/jmol-dev/bobtest/t.jvxl
isosurface1 created  with cutoff=0.02001; isosurface count: 1
isosurface full data range -0.007748252 to 10.191908 with color scheme
spanning -0.007748252 to 10.191908
1 id:isosurface1; model:0.0; vertices:1982; polygons:3960; visible:true;
dataRange:[-0.007748252, 10.191908, -0.007748252, 10.191908];
title:isosurface t.jvxl;

$




> You released 14.15.1, we installed it (not online), along with
> esomeprazole (chiral S). Configuration shows up but no double bonds when
> installed under EZ or EZ and RS groups.  We are working on it. Any
> thoughts?
>

Some aspects of chirality were broken in 14.15.1. I think. See most recent
at
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.15/Jmol%2014.15.2/



>  Fred
>
> PS: This message precedes “follow-up”.
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>


-- 
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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Re: [Jmol-users] Follow up ?

[Robert Hanson]

Yes, that's right. But you need to use what I just released, 14.15.2. Note
that the version of OPSIN used at NCI cannot handle that 4R designation:

$ load "$(4R,2Z,5E)-4-methylhepta-2,5-diene"
script ERROR: java.io.FileNotFoundException:
https://cactus.nci.nih.gov/chemical/structure/(4R,2Z,5E)-4-methylhepta-2,5-diene/file?format=sdf=true

$ load "$(2Z,5E)-4-methylhepta-2,5-diene"
C8H14

$ calculate chirality
$ print {chirality != ""}.label("%i%[chirality]").join("")
2R3Z4Z6E7E

(Note that Jmol assigns E/Z, R/S, and M/P chirality to both ends of an
alkene, cumulene, or atropisomeric bond, and that these numbers are not the
same as in the name.)

​Bob
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Re: [Jmol-users] Jmol 14.15.1

[Robert Hanson]

Fred, what's your story? I'm reading and writing Gaussian cube files.
Example?

On Fri, Apr 28, 2017 at 3:29 PM, fziegler <frederick.zieg...@yale.edu>
wrote:

> Bob and Bruce:
>
> Bruce: Happy to see writing jvxl files working for you. No luck here with
> 14.15.1 using Gaussian cube files. Any thoughts. Fred
>
>
>
> On Apr 28, 2017, at 2:46 PM, Bruce Tattershall <
> bruce.tattersh...@newcastle.ac.uk> wrote:
>
> Bob
>
> The version you published yesterday works fine for finding chirality in my
> organo PS cage compounds
> (e.g. with 67 atoms), both in JSmol and in Jmol_S.
>
> The problem with writing mo  jvxl files is also fixed for me.
>
> Contour plots on a plane .pmesh files do come back with the same colour
> scheme they had before saving,
> but if one changes this to colour scheme bw, I have not found any way to
> switch back to the saved colours,
> other than reloading the file.  The original isosurface plane was coloured
> with colour scheme bwr, but if
> I reapply this, the contours come out all white.   Any ideas?
>
> Thanks
>Bruce
>
> *From:* Robert Hanson [mailto:hans...@stolaf.edu <hans...@stolaf.edu>]
> *Sent:* 28 April 2017 19:11
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] Jmol 14.15.1
>
>
> OK, that version is broken for CIP chirality determination in JavaScript.
> Ran into an odd Java->JavaScript problem that requires recompilation.
> Simple structures will work, but more advanced issues will cause atoms to
> not display a chirality designation with label %[chirality]. JavaScript
> only; Java is fine.
>
>
> Bob
>
> On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Jmol.___JmolVersion="14.15.1" // 4/28/17
>
> bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks,
> and cartoonSteps
> bug fix: write MO broken
> bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails
>
> new feature: x.split(true)
>  -- does a white-space token split of the string value of x
>
> new feature: MOL/SDF reader reads M  ISO  lines for isotopes
> new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal
> pyramidal and tetrahedral
> new feature: CIP chirality adds imine and diazine E/Z chirality
>
> bug fix: CIP chirality broken for carbonyl groups
> bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
>
> code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds
>   - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/
> Jmol-datafiles/cip/
> code: CIP optimizations
>
>
>
> --
>
> 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
>
>
>
> --
>
> 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
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org>!
> http://sdm.link/slashdot___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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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Re: [Jmol-users] Jmol 14.15.1

[Robert Hanson]

OK, that version is broken for CIP chirality determination in JavaScript.
Ran into an odd Java->JavaScript problem that requires recompilation.
Simple structures will work, but more advanced issues will cause atoms to
not display a chirality designation with label %[chirality]. JavaScript
only; Java is fine.



Bob

On Thu, Apr 27, 2017 at 8:41 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Jmol.___JmolVersion="14.15.1" // 4/28/17
>
> bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks,
> and cartoonSteps
> bug fix: write MO broken
> bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails
>
> new feature: x.split(true)
>  -- does a white-space token split of the string value of x
>
> new feature: MOL/SDF reader reads M  ISO  lines for isotopes
> new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal
> pyramidal and tetrahedral
> new feature: CIP chirality adds imine and diazine E/Z chirality
>
> bug fix: CIP chirality broken for carbonyl groups
> bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
>
> code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds
>   - see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/
> Jmol-datafiles/cip/
> code: CIP optimizations
>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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[Jmol-users] Fwd: Important MathJax Information

[Robert Hanson]

FYI

-- Forwarded message --
From: Timothy Wallace 
Date: Fri, Apr 28, 2017 at 12:20 PM
Subject: Fwd: Important MathJax Information



On April 30th MathJax are closing their self-hosted CDN (Content Delivery
Network) services at *cdn.mathjax.org * and
*beta.mathjax.org
*. If your colleagues are linking to either of
these CDNs for MathJax functionality in any web pages/applications, they
will need to change the link(s) to point to an alternative CDN provider.
This should be a minor change and details on carrying this out are provided
below.


*Changing MathJax CDN: *We recommend changing to the cdnjs CDN. MathJax are
working with cdnjs to push out future releases.

You need to change the link to the CDN wherever it appears in your web
page/application code. For example, if you have been using the latest
MathJax version (v2.7.0) change the link text before the question mark as
below. Note that the url parameters (everything including and after the
“?”) should not be changed:

https://cdn.mathjax.org/mathjax/2.7-latest/MathJax.js
<https://cdn.mathjax.org/mathjax/2.7-latest/MathJax.js?>*?
<https://cdn.mathjax.org/mathjax/2.7-latest/MathJax.js?>...">
to
https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js
<https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?>*?
<https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?>
...">

This only applies where the CDN is being used to include MathJax
functionality. If the MathJax library is being used locally (i.e. has been
downloaded and linked to), then no change is required.

For further details, please see:
https://www.mathjax.org/cdn-shutting-down/
--
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[Jmol-users] Jmol 14.15.1

[Robert Hanson]

Jmol.___JmolVersion="14.15.1" // 4/28/17

bug fix: values not saved in state for cartoonBlockHeight, cartoonBlocks,
and cartoonSteps
bug fix: write MO broken
bug fix: set cartoonBlockHeight (for DSSR nucleic acid rendering) fails

new feature: x.split(true)
 -- does a white-space token split of the string value of x

new feature: MOL/SDF reader reads M  ISO  lines for isotopes
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal
pyramidal and tetrahedral
new feature: CIP chirality adds imine and diazine E/Z chirality

bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8

code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds
  - see
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
code: CIP optimizations



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

argh.  Broke chirality for ketones!

On Fri, Apr 21, 2017 at 11:27 AM, Robert Hanson <hans...@stolaf.edu> wrote:

>
>
> On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
> bruce.tattersh...@newcastle.ac.uk> wrote:
>
>> Dear Bob
>>
>>
>>
>> The chirality calculation is clearly useful.
>>
>>
>>
>> I have tried it on my chiral phosphorus compounds, e.g. as in
>>
>> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>>
>> and it finds the chiral carbons in the organic ligands and successfully
>> labels them (as R in this case),
>>
>> but it does not find the chirality of the phosphorus atoms to which they
>> are attached.
>>
>>
> It's a work in progress.
>
> Limitations:
>
>  no parallel chirality paths
>  not processing inositols correctly
>  no lone-pair business
>  standard E/Z, R/S, r/s only; no allenes, no planar asymmetry
>
>
>
>>
>> I have no idea of how this works, but would it be possible to extend it
>> easily to phosphorus chirality (for which
>>
>> one uses the same rules but counts the lone pair as lowest priority)?
>>
>>
> Lone pairs wouldn't be too difficult to add, particularly if they are
> limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
> add imine stereochemistry as well.
>
>
>
>>
>>
>> When I first got into measuring NMR spectra of diastereomers of such
>> compounds about 15 years ago,
>>
>> I found it very hard to get my inorganic chemist’s head around the
>> chirality implications.  It would
>>
>> have been very useful to have a tool to work it out for me.
>>
>>
>>
>> If you are going to elements other than carbon, then I guess that besides
>> phosphorus, the inorganic
>>
>> chemist’s favourite, the chirality at silicon, germanium and arsenic
>> could also be useful to people.
>>
>
> Silicon and ammonium are just like carbon, I think. As and P no problem.
>
> Definitely not going to higher valencies any time soon.
>
> Higher priorities are allenes and getting the darned inositol business
> working  correctly. But maybe P and S and As are so easy I should just do
> them
>
> Bob
>



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> Dear Bob
>
>
>
> The chirality calculation is clearly useful.
>
>
>
> I have tried it on my chiral phosphorus compounds, e.g. as in
>
> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>
> and it finds the chiral carbons in the organic ligands and successfully
> labels them (as R in this case),
>
> but it does not find the chirality of the phosphorus atoms to which they
> are attached.
>
>
It's a work in progress.

Limitations:

 no parallel chirality paths
 not processing inositols correctly
 no lone-pair business
 standard E/Z, R/S, r/s only; no allenes, no planar asymmetry



>
> I have no idea of how this works, but would it be possible to extend it
> easily to phosphorus chirality (for which
>
> one uses the same rules but counts the lone pair as lowest priority)?
>
>
Lone pairs wouldn't be too difficult to add, particularly if they are
limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
add imine stereochemistry as well.



>
>
> When I first got into measuring NMR spectra of diastereomers of such
> compounds about 15 years ago,
>
> I found it very hard to get my inorganic chemist’s head around the
> chirality implications.  It would
>
> have been very useful to have a tool to work it out for me.
>
>
>
> If you are going to elements other than carbon, then I guess that besides
> phosphorus, the inorganic
>
> chemist’s favourite, the chirality at silicon, germanium and arsenic could
> also be useful to people.
>

Silicon and ammonium are just like carbon, I think. As and P no problem.

Definitely not going to higher valencies any time soon.

Higher priorities are allenes and getting the darned inositol business
working  correctly. But maybe P and S and As are so easy I should just do
them

Bob
--
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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak  wrote:

> Bob;
>
> I am looking forward to exploring the new R/S and E/Z functionality; it's
> a great addition.
>
> Does this version include fix for "*spacefill ionic;lcaocartoon scale 1.0
> CAP unitcell "cpk";spacefill off" *which freezes the Jmol (Java) and
> leaves open surfaces (no "cap') on many unticell faces in JSmol?
>
>
yes, I think so. Please test. Also the fact that sometimes caps were not
completely closed.


> Thanks,
>
> PM
>
--
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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

OK - this is better:  Looking for the latest version? * Download
Jmol-14.14.1-binary.zip (69.7 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files> *

On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> hmm. something is missing there. I had to delete that and will upload
> again.
>
> On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson <hans...@stolaf.edu>
> wrote:
>
>> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>>
>> new feature: CALCULATE CHIRALITY {atom set}
>>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>>   -- continues with Rules 3-5, which require full-molecule analysis.
>>   -- work in progress:
>>  -- Rules 1 and 2 complete
>>  -- Rule 3 (E/Z) implemented
>>  -- Rule 4 partially implemented
>> -- simple linear sequences of R/S ok
>>  -- Rule 5 not implemented
>>   -- caveates
>>  -- no pseudochirality
>>  -- not cyclitols
>>  -- does not distinguish rings, so inserts "Z" into ring bonds
>>  -- only validated on
>>
>>   -- optionally limited to the given atom set (or the currently selected
>> atoms by default)
>>
>> new feature: set jmolInJSpecView
>>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
>> opened in Jmol
>>   -- default TRUE
>>
>> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
>> format)
>>   -- relatively compact format
>>   -- can speed up loading of meshes and contours
>>   -- for filled surfaces, use .jvxl instead
>>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>>   -- note that binary files are NOT RECOMMENDED for JSmol because some
>> platforms cannot read them locally
>>   -- example:
>>
>>   load $methane
>>   isosurface plane {0 0 0 1} map vdw contours 20
>>   write ISOSURFACE contour.pmb
>>   isosurface contour.pmb
>>
>>
>> bug fix: mesh capper producing gaps
>> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
>> 1, 2, and 3 (though still some questions about Rule 3)
>> bug fix: print getProperty("cifinfo") without file name fails
>>
>>
>>
>>
>> --
>> 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
>>
>>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

hmm. something is missing there. I had to delete that and will upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>
> new feature: CALCULATE CHIRALITY {atom set}
>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>   -- continues with Rules 3-5, which require full-molecule analysis.
>   -- work in progress:
>  -- Rules 1 and 2 complete
>  -- Rule 3 (E/Z) implemented
>  -- Rule 4 partially implemented
> -- simple linear sequences of R/S ok
>  -- Rule 5 not implemented
>   -- caveates
>  -- no pseudochirality
>  -- not cyclitols
>  -- does not distinguish rings, so inserts "Z" into ring bonds
>  -- only validated on
>
>   -- optionally limited to the given atom set (or the currently selected
> atoms by default)
>
> new feature: set jmolInJSpecView
>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
> opened in Jmol
>   -- default TRUE
>
> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
> format)
>   -- relatively compact format
>   -- can speed up loading of meshes and contours
>   -- for filled surfaces, use .jvxl instead
>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>   -- note that binary files are NOT RECOMMENDED for JSmol because some
> platforms cannot read them locally
>   -- example:
>
>   load $methane
>   isosurface plane {0 0 0 1} map vdw contours 20
>   write ISOSURFACE contour.pmb
>   isosurface contour.pmb
>
>
> bug fix: mesh capper producing gaps
> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
> 1, 2, and 3 (though still some questions about Rule 3)
> bug fix: print getProperty("cifinfo") without file name fails
>
>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

link for this release: * Download Jmol-14.14.1-binary.zip (65.0 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files> *

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>
> new feature: CALCULATE CHIRALITY {atom set}
>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>   -- continues with Rules 3-5, which require full-molecule analysis.
>   -- work in progress:
>  -- Rules 1 and 2 complete
>  -- Rule 3 (E/Z) implemented
>  -- Rule 4 partially implemented
> -- simple linear sequences of R/S ok
>  -- Rule 5 not implemented
>   -- caveates
>  -- no pseudochirality
>  -- not cyclitols
>  -- does not distinguish rings, so inserts "Z" into ring bonds
>  -- only validated on
>
>   -- optionally limited to the given atom set (or the currently selected
> atoms by default)
>
> new feature: set jmolInJSpecView
>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
> opened in Jmol
>   -- default TRUE
>
> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
> format)
>   -- relatively compact format
>   -- can speed up loading of meshes and contours
>   -- for filled surfaces, use .jvxl instead
>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>   -- note that binary files are NOT RECOMMENDED for JSmol because some
> platforms cannot read them locally
>   -- example:
>
>   load $methane
>   isosurface plane {0 0 0 1} map vdw contours 20
>   write ISOSURFACE contour.pmb
>   isosurface contour.pmb
>
>
> bug fix: mesh capper producing gaps
> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
> 1, 2, and 3 (though still some questions about Rule 3)
> bug fix: print getProperty("cifinfo") without file name fails
>
>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Jmol 14.14.1

[Robert Hanson]

Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently selected
atoms by default)

new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
format)
  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails




-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] R: Jmol 14.13.1

[Robert Hanson]

HOMO looks great to me. Maybe just a problem with your browser cache. This
seems to be a downside of HTML5. For some reason .js files do not update
even though they are changed unless (some users?) do a cache clearing.

On Sat, Apr 15, 2017 at 9:49 AM, pinostricc...@alice.it <
pinostricc...@alice.it> wrote:

> Happy Easter to everybody. I found out a problem on my site after i
> upgraded to jsmol 1.13.1
> On my pages like http://pinostriccoli.altervista.org/?p=5206, i cannot
> see anymore surfaces on MO.
> Any robem with upgrade or with new Jsmol?
>  Pino
>
> Messaggio originale
> Da: hans...@stolaf.edu
> Data: 10-apr-2017 4.44
> A: "jmol-users@lists.sourceforge.net"
> Ogg: [Jmol-users] Jmol 14.13.1
>
> https://sourceforge.net/projects/jmol/files/Jmol/
> Version%2014.13/Jmol%2014.13.1/
>
> Jmol.___JmolVersion="14.13.1" // 2017.04.09
>
> new feature: set labelfor {atomset} "value"
>  -- allows setting of label without changing current selection
>  -- uses same syntax as LABEL command after {atomset}
>  -- for example:
>
>set labelfor @atoms @myLabel
>set labelfor {atomno <= 3} @{["a","b","c"]}
>set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"
>
> new feature: MOL V2000 reader loads >  blocks into _M.molData
>
> bug fix: {*}.chirality with triple bonds fails
> bug fix: {*}.chirality fix for duplicated atoms check
>
> bug fix: dotted line has annoying extra dot: measure ID m @1 @4 radius 0.1
>
> bug fix: NBO H-BOND and MODEL focus issues
>
>
>
> --
> 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
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Jcamp-mol setup

[Robert Hanson]

That said, it's a very good idea, and I'm sure very easy to implement.

On Thu, Apr 13, 2017 at 8:11 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> no, there isn't, but you can adjust the size of that window to anything
> you want just be dragging the bars around it or resizing the window.
>
> On Wed, Apr 12, 2017 at 2:24 PM, PASCAL Andrew <andrew.pas...@cea.fr>
> wrote:
>
>> When connecting a spectrum with a molecular animation in a JCamp-MOL
>> file, is there any way to default to using the main Jmol window for the
>> structure, rather than the JSpecView side panel?
>>
>> Thanks,
>>
>> andy pascal (andrew.pas...@cea.fr)
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] Jcamp-mol setup

[Robert Hanson]

no, there isn't, but you can adjust the size of that window to anything you
want just be dragging the bars around it or resizing the window.

On Wed, Apr 12, 2017 at 2:24 PM, PASCAL Andrew  wrote:

> When connecting a spectrum with a molecular animation in a JCamp-MOL file,
> is there any way to default to using the main Jmol window for the
> structure, rather than the JSpecView side panel?
>
> Thanks,
>
> andy pascal (andrew.pas...@cea.fr)
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] atom-label tooltips

[Robert Hanson]

hover off

On Wed, Apr 12, 2017 at 1:15 PM, Pshemak Maslak  wrote:

> Is there a way to turn off atom-label tooltips that show on hover (above
> an atom)?
>
> I would like to hide their identity in some totally artificial structures.
>
> Thanks,
>
> PM
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] Jmol 14.13.1

[Robert Hanson]

OK, I know how I my comparison method violated the general contract. Very
surprised this ever worked!

On Mon, Apr 10, 2017 at 1:37 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Pshemak,
>
> Gotta love this error message:
>
> java.lang.IllegalArgumentException: Comparison method violates its
> general contract!
>
> I'll check on this.
>
> Bob
>
>
> On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>
>> Otis and Dean,,
>>
>> Thanks for the explanation. I was indeed able to find the whole command
>> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
>> *) * in the documentation (in the "cpk" example of lcaoCartoons).
>>
>> I think I understand it better now. The "spacefill" spheres are replaced
>> with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell"
>> as slabbing planes.
>>
>> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in
>> the center of the cell and one Na+  in the corner (which is properly
>> CAP-ed).
>>
>> However when I load {1 1 1} cell to get all ions within the cell, the
>> Jmol (desktop Java app) freezes. I tried the newest version (14.13.1) an an
>> older one (14.8.0) with the same results.
>>
>> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which
>> show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell
>> "cpk";spacefill off"  froze Jmol as well.
>>
>> Any suggestions?
>>
>> Thanks for your help.
>>
>> PM
>>
>>
>>
>> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>>
>> Pshemak,
>>
>> The CAP part is discussed here:
>>
>> https://chemapps.stolaf.edu/jmol/docs/index.htm?=
>> 1=14.6#isosurface
>>
>> Scroll down until you see CAP listing.
>>
>> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>>
>> Dean, the main reason I'm jumping in here is the display unitcell
>> command. Is that a legal Jmol Script command? After loading a CIF file, I
>> thought that you had to do something like this to get the unit cell:
>>
>> save orientation; load "" {444 666 1}; set displayCellParameters
>> false;restore orientation; unitcell on; display cell=555; center visible;
>> zoom 200;
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>>
>> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>>
>> Thank you Dean,
>>
>> I do not understand the
>>
>> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;
>>
>>
>> part of the command. Is it documented in https://chemapps.stolaf.edu
>> /jmol/docs/  ?
>>
>> Thanks,
>>
>> PM
>>
>>
>> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>>
>> Yes - I have an example at: http://crystals.otterbein.
>> edu/packing/index.html
>>
>> Pick structure from the left menu and then click the “Show Contents of
>> One Unit Cell”. Works beautifully!
>>
>> The commands are:
>> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP
>> unitcell 'cpk'; spacefill 1%;
>>
>> Dean Johnston
>>
>> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
>>
>>
>> Can the "slab" command be used to produce presentations equivalent to the
>> image linked below?
>>
>> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/F
>> ile:CCC_crystal_cell_(opaque).svg
>>
>> If so, any suggestions on how to do that would be appreciated.
>>
>> Thanks,
>>
>> PM
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sd
>> m.link/slashdot___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org/>! 
>> http://sdm.link/slashdot
>>
>>
>>
>> ___
>> Jmol-users mailing 

Re: [Jmol-users] Jmol 14.13.1

[Robert Hanson]

Pshemak,

Gotta love this error message:

java.lang.IllegalArgumentException: Comparison method violates its general
contract!

I'll check on this.

Bob


On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak  wrote:

> Otis and Dean,,
>
> Thanks for the explanation. I was indeed able to find the whole command
> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
> *) * in the documentation (in the "cpk" example of lcaoCartoons).
>
> I think I understand it better now. The "spacefill" spheres are replaced
> with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell"
> as slabbing planes.
>
> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in
> the center of the cell and one Na+  in the corner (which is properly
> CAP-ed).
>
> However when I load {1 1 1} cell to get all ions within the cell, the Jmol
> (desktop Java app) freezes. I tried the newest version (14.13.1) an an
> older one (14.8.0) with the same results.
>
> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which
> show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell
> "cpk";spacefill off"  froze Jmol as well.
>
> Any suggestions?
>
> Thanks for your help.
>
> PM
>
>
>
> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>
> Pshemak,
>
> The CAP part is discussed here:
>
> https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#
> isosurface
>
> Scroll down until you see CAP listing.
>
> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>
> Dean, the main reason I'm jumping in here is the display unitcell command.
> Is that a legal Jmol Script command? After loading a CIF file, I thought
> that you had to do something like this to get the unit cell:
>
> save orientation; load "" {444 666 1}; set displayCellParameters
> false;restore orientation; unitcell on; display cell=555; center visible;
> zoom 200;
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak  wrote:
>
> Thank you Dean,
>
> I do not understand the
>
> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;
>
>
> part of the command. Is it documented in https://chemapps.stolaf.
> edu/jmol/docs/  ?
>
> Thanks,
>
> PM
>
>
> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>
> Yes - I have an example at: http://crystals.otterbein.
> edu/packing/index.html
>
> Pick structure from the left menu and then click the “Show Contents of One
> Unit Cell”. Works beautifully!
>
> The commands are:
> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell
> 'cpk'; spacefill 1%;
>
> Dean Johnston
>
> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
>
>
> Can the "slab" command be used to produce presentations equivalent to the
> image linked below?
>
> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/
> File:CCC_crystal_cell_(opaque).svg
>
> If so, any suggestions on how to do that would be appreciated.
>
> Thanks,
>
> PM
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org ! http://
> sdm.link/slashdot___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org ! 
> http://sdm.link/slashdot
>
>
>
> ___
> Jmol-users mailing 
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org ! http://
> sdm.link/slashdot___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> ___
> Jmol-users mailing 
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> 

[Jmol-users] Jmol 14.13.1

[Robert Hanson]

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.13/Jmol%2014.13.1/

Jmol.___JmolVersion="14.13.1" // 2017.04.09

new feature: set labelfor {atomset} "value"
 -- allows setting of label without changing current selection
 -- uses same syntax as LABEL command after {atomset}
 -- for example:

   set labelfor @atoms @myLabel
   set labelfor {atomno <= 3} @{["a","b","c"]}
   set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"

new feature: MOL V2000 reader loads >  blocks into _M.molData

bug fix: {*}.chirality with triple bonds fails
bug fix: {*}.chirality fix for duplicated atoms check

bug fix: dotted line has annoying extra dot: measure ID m @1 @4 radius 0.1

bug fix: NBO H-BOND and MODEL focus issues



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality

[Robert Hanson]

I need to get you a version that has alkynes fixed. I think what is up
there now does not have that.

On Sun, Apr 9, 2017 at 2:16 PM, pinostricc...@alice.it <
pinostricc...@alice.it> wrote:

> Great job, Bob. Really. I will implement it on my website for my students
> to use.
> Sometime imagining molecules in 3D is not that easy :)
> @Pierluigi. I was referring to your pages too with my compliment
> Pino
>
> Messaggio originale
> Da: hans...@stolaf.edu
> Data: 9-apr-2017 14.55
> A: "jmol-users@lists.sourceforge.net"<jmol-users@lists.sourceforge.net>
> Ogg: Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality
>
>
> I will release another version of Jmol later today that has been pretty
> heavily validated using some excellent  extreme examples provided by Mikko
> Vainio that caught a couple of bugs.
>
> On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Many thanks, Bob!
>>
>> Bye!
>>
>> Pierluigi
>>
>>
>>
>> Il 08/04/2017 03:54, Robert Hanson ha scritto:
>>
>> https://sourceforge.net/projects/jmol/files/Jmol/Version%201
>> 4.12/Jmol%2014.12.1/
>>
>>
>> Jmol.___JmolVersion="14.12.1"
>>
>> bug fix: NBO update
>> bug fix: JavaScript bug - missing  Math.signum(f) - causes
>> {atom}.chirality to not work in JSmol
>>
>> JmolVersion="14.12.0" // 2017-04-06
>>
>> new feature: {atom}.chirality
>>   -- also SELECT chirality = 'R'# or SELECT chirality != ""
>>   -- uses Cahn-Ingold-Prelog rules to assign R or S to a carbon center
>>   -- ignores sulfur chirality
>>   -- may not fully implement high symmetry cases
>>   -- not fully tested
>>
>>
>>
>> --
>> 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
>>
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> ___
>> Jmol-users mailing 
>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

[Robert Hanson]

I will release another version of Jmol later today that has been pretty
heavily validated using some excellent  extreme examples provided by Mikko
Vainio that caught a couple of bugs.

On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it> wrote:

> Many thanks, Bob!
>
> Bye!
>
> Pierluigi
>
>
>
> Il 08/04/2017 03:54, Robert Hanson ha scritto:
>
> https://sourceforge.net/projects/jmol/files/Jmol/Version%
> 2014.12/Jmol%2014.12.1/
>
>
> Jmol.___JmolVersion="14.12.1"
>
> bug fix: NBO update
> bug fix: JavaScript bug - missing  Math.signum(f) - causes
> {atom}.chirality to not work in JSmol
>
> JmolVersion="14.12.0" // 2017-04-06
>
> new feature: {atom}.chirality
>   -- also SELECT chirality = 'R'# or SELECT chirality != ""
>   -- uses Cahn-Ingold-Prelog rules to assign R or S to a carbon center
>   -- ignores sulfur chirality
>   -- may not fully implement high symmetry cases
>   -- not fully tested
>
>
>
> --
> 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
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> ___
> Jmol-users mailing 
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Jmol 14.12.1 released -- R/S chirality

[Robert Hanson]

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/


Jmol.___JmolVersion="14.12.1"

bug fix: NBO update
bug fix: JavaScript bug - missing  Math.signum(f) - causes {atom}.chirality
to not work in JSmol

JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- also SELECT chirality = 'R'# or SELECT chirality != ""
  -- uses Cahn-Ingold-Prelog rules to assign R or S to a carbon center
  -- ignores sulfur chirality
  -- may not fully implement high symmetry cases
  -- not fully tested



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

[Robert Hanson]

OK, that is fixed in
https://sourceforge.net/p/jsmol/code/HEAD/tree/trunk/dist and at
https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm

On Fri, Apr 7, 2017 at 12:50 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> That is to say, I just found a mistake in the way the JavaScript version
> is working. Looking into that now. Java is OK.
>
> On Fri, Apr 7, 2017 at 12:46 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> ps -- *before I find it*
>>
>> On Fri, Apr 7, 2017 at 12:42 PM, Robert Hanson <hans...@stolaf.edu>
>> wrote:
>>
>>> Super. Tell them there is a prize for the first student who finds a
>>> mistake in assignment.
>>>
>>>
>>>
>>> On Fri, Apr 7, 2017 at 1:52 AM, Pierluigi Quagliotto <
>>> pierluigi.quaglio...@unito.it> wrote:
>>>
>>>> Dear Bob,
>>>>
>>>> many thanks for it!
>>>>
>>>> In this weekend I will try  to update my page and make proper test.
>>>> Once I will be able to put the page on the production site I will put my
>>>> student to make extensive tests, with both simple and complex molecules, to
>>>> help you to validate the novel function. I'll let you know when the page
>>>> will be ready, just to see it "at work".
>>>>
>>>> Bye!
>>>>
>>>> Pierluigi Quagliotto
>>>>
>>>>
>>>> Il 07/04/2017 01:21, Robert Hanson ha scritto:
>>>>
>>>> This is done.
>>>>
>>>>
>>>> Jmol.___JmolVersion="14.12.0" // 2017-04-06
>>>>
>>>> new feature: {atom}.chirality
>>>>   -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
>>>>   -- ignores sulfur chirality
>>>>   -- may not fully implement high symmetry cases
>>>>   -- not fully tested
>>>>   -- Checked using:
>>>>
>>>> function checkchiral(m) {
>>>>   if (m)  load @m
>>>>   background label yellow
>>>>   color labels black
>>>>   select _C
>>>>   label %[atomname]
>>>>   refresh
>>>>   var b = {_C}
>>>>   for (var a in b) {
>>>> var c = a.chirality;
>>>> print _smilesString + " " + a + c
>>>> if (c) {
>>>>select a
>>>>c = a.atomname + " " + c
>>>>label @c
>>>> }
>>>>   }
>>>>   select *
>>>> }
>>>>
>>>> checkchiral("$(R)-glycidol")
>>>> delay 1
>>>> checkchiral("$glucose")
>>>> delay 1
>>>> checkchiral("$(2S,3R)-2,3-oxiranediol")
>>>> delay 1
>>>> checkchiral("$(S)-2-butanol")
>>>> delay 1
>>>> checkchiral("$(R)-2-butanol")
>>>> delay 1
>>>> checkchiral("$(2S,3R)-2,3-butanediol")
>>>> delay 1
>>>> checkchiral("$(2S,3S)-2,3-butanediol")
>>>> delay 1
>>>> checkchiral("$(2R,3R)-2,3-butanediol")
>>>> delay 1
>>>> checkchiral("$(2R,3S)-2,3-butanediol")
>>>> delay 1
>>>> checkchiral("$1,4-dimethylcyclohexane")
>>>> delay 1
>>>> checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain
>>>> R
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
>>>> pierluigi.quaglio...@unito.it> wrote:
>>>>
>>>>> Dear Bob,
>>>>>
>>>>> many thanks for your answer.
>>>>> I had a look to the paper, but it is very concise, so I would be in
>>>>> doubt about how to proceed. If we (I and a young fellowship who should 
>>>>> help
>>>>> me for the site in next months) can envisage what (and how to do) we will
>>>>> let you know some more. Obviously, if this feature will become available 
>>>>> in
>>>>> JMol/JSMol, this should be nice and also a great improvement for teaching!
>>>>>
>>>>> I will start to introduce the page I prepared in the production site,
>>>>> just to let student to familiarize with the common procedure used to
>>>>> approach to chirality determination. If some improvement about chirality
>>>>> determination will be available in JMol

Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

[Robert Hanson]

That is to say, I just found a mistake in the way the JavaScript version is
working. Looking into that now. Java is OK.

On Fri, Apr 7, 2017 at 12:46 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> ps -- *before I find it*
>
> On Fri, Apr 7, 2017 at 12:42 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Super. Tell them there is a prize for the first student who finds a
>> mistake in assignment.
>>
>>
>>
>> On Fri, Apr 7, 2017 at 1:52 AM, Pierluigi Quagliotto <
>> pierluigi.quaglio...@unito.it> wrote:
>>
>>> Dear Bob,
>>>
>>> many thanks for it!
>>>
>>> In this weekend I will try  to update my page and make proper test. Once
>>> I will be able to put the page on the production site I will put my student
>>> to make extensive tests, with both simple and complex molecules, to help
>>> you to validate the novel function. I'll let you know when the page will be
>>> ready, just to see it "at work".
>>>
>>> Bye!
>>>
>>> Pierluigi Quagliotto
>>>
>>>
>>> Il 07/04/2017 01:21, Robert Hanson ha scritto:
>>>
>>> This is done.
>>>
>>>
>>> Jmol.___JmolVersion="14.12.0" // 2017-04-06
>>>
>>> new feature: {atom}.chirality
>>>   -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
>>>   -- ignores sulfur chirality
>>>   -- may not fully implement high symmetry cases
>>>   -- not fully tested
>>>   -- Checked using:
>>>
>>> function checkchiral(m) {
>>>   if (m)  load @m
>>>   background label yellow
>>>   color labels black
>>>   select _C
>>>   label %[atomname]
>>>   refresh
>>>   var b = {_C}
>>>   for (var a in b) {
>>> var c = a.chirality;
>>> print _smilesString + " " + a + c
>>> if (c) {
>>>select a
>>>c = a.atomname + " " + c
>>>label @c
>>> }
>>>   }
>>>   select *
>>> }
>>>
>>> checkchiral("$(R)-glycidol")
>>> delay 1
>>> checkchiral("$glucose")
>>> delay 1
>>> checkchiral("$(2S,3R)-2,3-oxiranediol")
>>> delay 1
>>> checkchiral("$(S)-2-butanol")
>>> delay 1
>>> checkchiral("$(R)-2-butanol")
>>> delay 1
>>> checkchiral("$(2S,3R)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$(2S,3S)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$(2R,3R)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$(2R,3S)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$1,4-dimethylcyclohexane")
>>> delay 1
>>> checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
>>>
>>>
>>>
>>>
>>> On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
>>> pierluigi.quaglio...@unito.it> wrote:
>>>
>>>> Dear Bob,
>>>>
>>>> many thanks for your answer.
>>>> I had a look to the paper, but it is very concise, so I would be in
>>>> doubt about how to proceed. If we (I and a young fellowship who should help
>>>> me for the site in next months) can envisage what (and how to do) we will
>>>> let you know some more. Obviously, if this feature will become available in
>>>> JMol/JSMol, this should be nice and also a great improvement for teaching!
>>>>
>>>> I will start to introduce the page I prepared in the production site,
>>>> just to let student to familiarize with the common procedure used to
>>>> approach to chirality determination. If some improvement about chirality
>>>> determination will be available in JMol/JSMol in the future, I will use it
>>>> enthusiastically. In the last two-three years, as long as my site teaching
>>>> site was produced and developed, I observed great improvement in the
>>>> student's ability to comprehend concepts and use them in solving problems,
>>>> so I will try to do all my best to make continuous site improvements, as
>>>> far as I am able to deal with programming.
>>>>
>>>> Many thanks again for the time you dedicate to me,
>>>>
>>>> Bye!
>>>>
>>>> Pierluigi
>>>>
>>>>
>>>>
>>>>
>>>>
>>&

Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

[Robert Hanson]

ps -- *before I find it*

On Fri, Apr 7, 2017 at 12:42 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> Super. Tell them there is a prize for the first student who finds a
> mistake in assignment.
>
>
>
> On Fri, Apr 7, 2017 at 1:52 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear Bob,
>>
>> many thanks for it!
>>
>> In this weekend I will try  to update my page and make proper test. Once
>> I will be able to put the page on the production site I will put my student
>> to make extensive tests, with both simple and complex molecules, to help
>> you to validate the novel function. I'll let you know when the page will be
>> ready, just to see it "at work".
>>
>> Bye!
>>
>> Pierluigi Quagliotto
>>
>>
>> Il 07/04/2017 01:21, Robert Hanson ha scritto:
>>
>> This is done.
>>
>>
>> Jmol.___JmolVersion="14.12.0" // 2017-04-06
>>
>> new feature: {atom}.chirality
>>   -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
>>   -- ignores sulfur chirality
>>   -- may not fully implement high symmetry cases
>>   -- not fully tested
>>   -- Checked using:
>>
>> function checkchiral(m) {
>>   if (m)  load @m
>>   background label yellow
>>   color labels black
>>   select _C
>>   label %[atomname]
>>   refresh
>>   var b = {_C}
>>   for (var a in b) {
>> var c = a.chirality;
>> print _smilesString + " " + a + c
>> if (c) {
>>select a
>>c = a.atomname + " " + c
>>label @c
>> }
>>   }
>>   select *
>> }
>>
>> checkchiral("$(R)-glycidol")
>> delay 1
>> checkchiral("$glucose")
>> delay 1
>> checkchiral("$(2S,3R)-2,3-oxiranediol")
>> delay 1
>> checkchiral("$(S)-2-butanol")
>> delay 1
>> checkchiral("$(R)-2-butanol")
>> delay 1
>> checkchiral("$(2S,3R)-2,3-butanediol")
>> delay 1
>> checkchiral("$(2S,3S)-2,3-butanediol")
>> delay 1
>> checkchiral("$(2R,3R)-2,3-butanediol")
>> delay 1
>> checkchiral("$(2R,3S)-2,3-butanediol")
>> delay 1
>> checkchiral("$1,4-dimethylcyclohexane")
>> delay 1
>> checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
>>
>>
>>
>>
>> On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
>> pierluigi.quaglio...@unito.it> wrote:
>>
>>> Dear Bob,
>>>
>>> many thanks for your answer.
>>> I had a look to the paper, but it is very concise, so I would be in
>>> doubt about how to proceed. If we (I and a young fellowship who should help
>>> me for the site in next months) can envisage what (and how to do) we will
>>> let you know some more. Obviously, if this feature will become available in
>>> JMol/JSMol, this should be nice and also a great improvement for teaching!
>>>
>>> I will start to introduce the page I prepared in the production site,
>>> just to let student to familiarize with the common procedure used to
>>> approach to chirality determination. If some improvement about chirality
>>> determination will be available in JMol/JSMol in the future, I will use it
>>> enthusiastically. In the last two-three years, as long as my site teaching
>>> site was produced and developed, I observed great improvement in the
>>> student's ability to comprehend concepts and use them in solving problems,
>>> so I will try to do all my best to make continuous site improvements, as
>>> far as I am able to deal with programming.
>>>
>>> Many thanks again for the time you dedicate to me,
>>>
>>> Bye!
>>>
>>> Pierluigi
>>>
>>>
>>>
>>>
>>>
>>>
>>> Il 06/04/2017 14:29, Robert Hanson ha scritto:
>>>
>>>
>>>
>>> On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto <
>>> pierluigi.quaglio...@unito.it> wrote:
>>>
>>>> Dear All,
>>>>
>>>> I prepared a page for students (on my developing server:
>>>> http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-
>>>> sulla-chiralita),
>>>> in which they can:
>>>>
>>>> 1) write down an organic molecule in  JSME
>>>>
>>>> 2) submit it to JSmol
>>>>
>>>> 3) attribu

Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

[Robert Hanson]

Super. Tell them there is a prize for the first student who finds a mistake
in assignment.



On Fri, Apr 7, 2017 at 1:52 AM, Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it> wrote:

> Dear Bob,
>
> many thanks for it!
>
> In this weekend I will try  to update my page and make proper test. Once I
> will be able to put the page on the production site I will put my student
> to make extensive tests, with both simple and complex molecules, to help
> you to validate the novel function. I'll let you know when the page will be
> ready, just to see it "at work".
>
> Bye!
>
> Pierluigi Quagliotto
>
>
> Il 07/04/2017 01:21, Robert Hanson ha scritto:
>
> This is done.
>
>
> Jmol.___JmolVersion="14.12.0" // 2017-04-06
>
> new feature: {atom}.chirality
>   -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
>   -- ignores sulfur chirality
>   -- may not fully implement high symmetry cases
>   -- not fully tested
>   -- Checked using:
>
> function checkchiral(m) {
>   if (m)  load @m
>   background label yellow
>   color labels black
>   select _C
>   label %[atomname]
>   refresh
>   var b = {_C}
>   for (var a in b) {
> var c = a.chirality;
> print _smilesString + " " + a + c
> if (c) {
>select a
>c = a.atomname + " " + c
>label @c
> }
>   }
>   select *
> }
>
> checkchiral("$(R)-glycidol")
> delay 1
> checkchiral("$glucose")
> delay 1
> checkchiral("$(2S,3R)-2,3-oxiranediol")
> delay 1
> checkchiral("$(S)-2-butanol")
> delay 1
> checkchiral("$(R)-2-butanol")
> delay 1
> checkchiral("$(2S,3R)-2,3-butanediol")
> delay 1
> checkchiral("$(2S,3S)-2,3-butanediol")
> delay 1
> checkchiral("$(2R,3R)-2,3-butanediol")
> delay 1
> checkchiral("$(2R,3S)-2,3-butanediol")
> delay 1
> checkchiral("$1,4-dimethylcyclohexane")
> delay 1
> checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
>
>
>
>
> On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear Bob,
>>
>> many thanks for your answer.
>> I had a look to the paper, but it is very concise, so I would be in doubt
>> about how to proceed. If we (I and a young fellowship who should help me
>> for the site in next months) can envisage what (and how to do) we will let
>> you know some more. Obviously, if this feature will become available in
>> JMol/JSMol, this should be nice and also a great improvement for teaching!
>>
>> I will start to introduce the page I prepared in the production site,
>> just to let student to familiarize with the common procedure used to
>> approach to chirality determination. If some improvement about chirality
>> determination will be available in JMol/JSMol in the future, I will use it
>> enthusiastically. In the last two-three years, as long as my site teaching
>> site was produced and developed, I observed great improvement in the
>> student's ability to comprehend concepts and use them in solving problems,
>> so I will try to do all my best to make continuous site improvements, as
>> far as I am able to deal with programming.
>>
>> Many thanks again for the time you dedicate to me,
>>
>> Bye!
>>
>> Pierluigi
>>
>>
>>
>>
>>
>>
>> Il 06/04/2017 14:29, Robert Hanson ha scritto:
>>
>>
>>
>> On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto <
>> pierluigi.quaglio...@unito.it> wrote:
>>
>>> Dear All,
>>>
>>> I prepared a page for students (on my developing server:
>>> http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-
>>> sulla-chiralita),
>>> in which they can:
>>>
>>> 1) write down an organic molecule in  JSME
>>>
>>> 2) submit it to JSmol
>>>
>>> 3) attribute the Cahn-Ingold-Prelog priority to each group by selecting
>>> the first atom of each group which is attached to the Chiral Carbon and
>>> clicking on a button that create a label for that atom.
>>>
>>> 4) reorientate properly the molecule, in order to be able to assign the
>>> R / S configuration for chirality.
>>>
>>> This is enough for me to use in classroom just to show how one should
>>> proceed to work on exercises.
>>>
>>>
>>> My question is: Is there a way to obtain priority (by CIP rules) for
>>> each group attached to a 

Re: [Jmol-users] R: check R/S chirality with Jmol

[Robert Hanson]

I've added a "show R/S" button at
https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm

It just runs

label %[chirality]
background labels yellow



On Fri, Apr 7, 2017 at 12:24 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> I have that fixed in JavaScript but want to add a couple more unrelated
> items before I release this the normal way. But you  can also get jsmol.zip
> here: https://sourceforge.net/p/jsmol/code/HEAD/tree/trunk/dist/  and it
> should be  working at the St. Olaf site. For example: <
> https://chemapps.stolaf.edu/jmol/jsmol/simple2.htm?load%
> 20$(R)-2-butanol;label%20%[chirality];background%20labels%20yellow;set%
> 20antialiasdisplay>
>
>
> On Fri, Apr 7, 2017 at 11:57 AM, pinostricc...@alice.it <
> pinostricc...@alice.it> wrote:
>
>> Wonderful implementation Bob and Pierluigi. Veru useful in Organich
>> Chemistry
>> Pino
>>
>> Messaggio originale
>> Da: hans...@stolaf.edu
>> Data: 7-apr-2017 4.25
>> A: "jmol-users@lists.sourceforge.net"<jmol-users@lists.sourceforge.net>
>> Ogg: [Jmol-users] check R/S chirality with Jmol
>>
>>
>>
>> * Download Jmol-14.12.0-binary.zip (69.3 MB)
>> <https://sourceforge.net/projects/jmol/files/latest/download?source=files> *
>>
>>
>> *Jmol now allows checking of R/S chirality. For example:*
>> load $(R)-glycidol
>> print {C1}.chirality
>>
>> *R*
>>
>> load $cholesterol
>> select on chirality != ""
>> label %[chirality]
>>
>> *8 atoms selected*
>>
>>
>> Thanks to Pierluigi Quagliotto for the suggestion to tackle this. It was
>> a good challenge getting it right.
>>
>> Please test!
>>
>> Bob
>>
>> --
>> 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
>>
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] R: check R/S chirality with Jmol

[Robert Hanson]

I have that fixed in JavaScript but want to add a couple more unrelated
items before I release this the normal way. But you  can also get jsmol.zip
here: https://sourceforge.net/p/jsmol/code/HEAD/tree/trunk/dist/  and it
should be  working at the St. Olaf site. For example: <
https://chemapps.stolaf.edu/jmol/jsmol/simple2.htm?load%20$(R)-2-butanol;label%20%[chirality];background%20labels%20yellow;set%20antialiasdisplay
>


On Fri, Apr 7, 2017 at 11:57 AM, pinostricc...@alice.it <
pinostricc...@alice.it> wrote:

> Wonderful implementation Bob and Pierluigi. Veru useful in Organich
> Chemistry
> Pino
>
> Messaggio originale
> Da: hans...@stolaf.edu
> Data: 7-apr-2017 4.25
> A: "jmol-users@lists.sourceforge.net"
> Ogg: [Jmol-users] check R/S chirality with Jmol
>
>
>
> * Download Jmol-14.12.0-binary.zip (69.3 MB)
>  *
>
>
> *Jmol now allows checking of R/S chirality. For example:*
> load $(R)-glycidol
> print {C1}.chirality
>
> *R*
>
> load $cholesterol
> select on chirality != ""
> label %[chirality]
>
> *8 atoms selected*
>
>
> Thanks to Pierluigi Quagliotto for the suggestion to tackle this. It was a
> good challenge getting it right.
>
> Please test!
>
> Bob
>
> --
> 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
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] check R/S chirality with Jmol

[Robert Hanson]

OK, I see. I used a Java Math function that I did not implement in
JavaScript. Easy fix...

On Fri, Apr 7, 2017 at 10:31 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> Hmm. I do know where that is coming from. Admittedly I had not tried it in
> JavaScript! Will do. Working  in Jmol.jar, right?
>
>
>
> On Fri, Apr 7, 2017 at 3:39 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear Bob,
>>
>> there is something working wrong with JSMol 14.12.0 working on my
>> developing site...
>>
>> I obtain an error in the console when trying to execute some commands.
>>
>> here below the message is always the same and appears when the first call
>> to the novel function is tried.
>>
>>
>>
>>
>>
>> *Jmol now allows checking of R/S chirality. For example: *
>> load $(R)-glycidol
>> print {C1}.chirality
>>
>> script ERROR: TypeError: The object does not support the property or the
>> method 'printStackTrace'
>>
>>
>> *R*
>>
>> load $cholesterol
>> select on chirality != ""
>>
>> script ERROR: TypeError: The object does not support the property or the
>> method 'printStackTrace'
>>
>> label %[chirality]
>>
>> *8 atoms selected*
>>
>>
>>
>> I simply transferred the jsmol dir on the server, as usual and gave
>> proper 755 permission and apache.apache ownership. JSMol seems to work fine
>> but ht euse of the new function gave this error.
>>
>> Bye,
>>
>> Pierluigi Quagliotto
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] check R/S chirality with Jmol

[Robert Hanson]

Hmm. I do know where that is coming from. Admittedly I had not tried it in
JavaScript! Will do. Working  in Jmol.jar, right?



On Fri, Apr 7, 2017 at 3:39 AM, Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it> wrote:

> Dear Bob,
>
> there is something working wrong with JSMol 14.12.0 working on my
> developing site...
>
> I obtain an error in the console when trying to execute some commands.
>
> here below the message is always the same and appears when the first call
> to the novel function is tried.
>
>
>
>
>
> *Jmol now allows checking of R/S chirality. For example: *
> load $(R)-glycidol
> print {C1}.chirality
>
> script ERROR: TypeError: The object does not support the property or the
> method 'printStackTrace'
>
>
> *R*
>
> load $cholesterol
> select on chirality != ""
>
> script ERROR: TypeError: The object does not support the property or the
> method 'printStackTrace'
>
> label %[chirality]
>
> *8 atoms selected*
>
>
>
> I simply transferred the jsmol dir on the server, as usual and gave proper
> 755 permission and apache.apache ownership. JSMol seems to work fine but ht
> euse of the new function gave this error.
>
> Bye,
>
> Pierluigi Quagliotto
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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[Jmol-users] check R/S chirality with Jmol

[Robert Hanson]

* Download Jmol-14.12.0-binary.zip (69.3 MB)
 *


*Jmol now allows checking of R/S chirality. For example:*
load $(R)-glycidol
print {C1}.chirality

*R*

load $cholesterol
select on chirality != ""
label %[chirality]

*8 atoms selected*


Thanks to Pierluigi Quagliotto for the suggestion to tackle this. It was a
good challenge getting it right.

Please test!

Bob

-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

[Robert Hanson]

This is done.


Jmol.___JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
  -- ignores sulfur chirality
  -- may not fully implement high symmetry cases
  -- not fully tested
  -- Checked using:

function checkchiral(m) {
  if (m)  load @m
  background label yellow
  color labels black
  select _C
  label %[atomname]
  refresh
  var b = {_C}
  for (var a in b) {
var c = a.chirality;
print _smilesString + " " + a + c
if (c) {
   select a
   c = a.atomname + " " + c
   label @c
}
  }
  select *
}

checkchiral("$(R)-glycidol")
delay 1
checkchiral("$glucose")
delay 1
checkchiral("$(2S,3R)-2,3-oxiranediol")
delay 1
checkchiral("$(S)-2-butanol")
delay 1
checkchiral("$(R)-2-butanol")
delay 1
checkchiral("$(2S,3R)-2,3-butanediol")
delay 1
checkchiral("$(2S,3S)-2,3-butanediol")
delay 1
checkchiral("$(2R,3R)-2,3-butanediol")
delay 1
checkchiral("$(2R,3S)-2,3-butanediol")
delay 1
checkchiral("$1,4-dimethylcyclohexane")
delay 1
checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R




On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it> wrote:

> Dear Bob,
>
> many thanks for your answer.
> I had a look to the paper, but it is very concise, so I would be in doubt
> about how to proceed. If we (I and a young fellowship who should help me
> for the site in next months) can envisage what (and how to do) we will let
> you know some more. Obviously, if this feature will become available in
> JMol/JSMol, this should be nice and also a great improvement for teaching!
>
> I will start to introduce the page I prepared in the production site, just
> to let student to familiarize with the common procedure used to approach to
> chirality determination. If some improvement about chirality determination
> will be available in JMol/JSMol in the future, I will use it
> enthusiastically. In the last two-three years, as long as my site teaching
> site was produced and developed, I observed great improvement in the
> student's ability to comprehend concepts and use them in solving problems,
> so I will try to do all my best to make continuous site improvements, as
> far as I am able to deal with programming.
>
> Many thanks again for the time you dedicate to me,
>
> Bye!
>
> Pierluigi
>
>
>
>
>
>
> Il 06/04/2017 14:29, Robert Hanson ha scritto:
>
>
>
> On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear All,
>>
>> I prepared a page for students (on my developing server:
>> http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-
>> sulla-chiralita),
>> in which they can:
>>
>> 1) write down an organic molecule in  JSME
>>
>> 2) submit it to JSmol
>>
>> 3) attribute the Cahn-Ingold-Prelog priority to each group by selecting
>> the first atom of each group which is attached to the Chiral Carbon and
>> clicking on a button that create a label for that atom.
>>
>> 4) reorientate properly the molecule, in order to be able to assign the
>> R / S configuration for chirality.
>>
>> This is enough for me to use in classroom just to show how one should
>> proceed to work on exercises.
>>
>>
>> My question is: Is there a way to obtain priority (by CIP rules) for
>> each group attached to a Chiral Carbon? Is it possible to use some JSmol
>> function(s) to obtain this information?
>>
>>
> ho, ho! No, sorry. Can't do that. But I love the idea. In principal the
> algorithm is not all that difficult.
> https://www.chemcomp.com/journal/chiral.htm Maybe it's time to add that...
>
>
>
>
>
>> If the answer is yes, this could help me to modify the page to give the
>> student the chance to explore the correct result by viewing a model with
>> correct priority labelling and also by clicking on a button which
>> activate a function that perform the check.
>>
>>
>> Sorry to bothering you...
>>
>>
>> Bye!
>>
>>
>> Pierluigi Quagliotto
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
>

Re: [Jmol-users] Cahn-Ingold-Prelog priority rules

[Robert Hanson]

On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it> wrote:

> Dear All,
>
> I prepared a page for students (on my developing server:
> http://5.135.186.232/STdM/index.php/it/esercizi/
> esercitarsi-sulla-chiralita),
> in which they can:
>
> 1) write down an organic molecule in  JSME
>
> 2) submit it to JSmol
>
> 3) attribute the Cahn-Ingold-Prelog priority to each group by selecting
> the first atom of each group which is attached to the Chiral Carbon and
> clicking on a button that create a label for that atom.
>
> 4) reorientate properly the molecule, in order to be able to assign the
> R / S configuration for chirality.
>
> This is enough for me to use in classroom just to show how one should
> proceed to work on exercises.
>
>
> My question is: Is there a way to obtain priority (by CIP rules) for
> each group attached to a Chiral Carbon? Is it possible to use some JSmol
> function(s) to obtain this information?
>
>
ho, ho! No, sorry. Can't do that. But I love the idea. In principal the
algorithm is not all that difficult.
https://www.chemcomp.com/journal/chiral.htm Maybe it's time to add that...





> If the answer is yes, this could help me to modify the page to give the
> student the chance to explore the correct result by viewing a model with
> correct priority labelling and also by clicking on a button which
> activate a function that perform the check.
>
>
> Sorry to bothering you...
>
>
> Bye!
>
>
> Pierluigi Quagliotto
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Followup to "Re: vibrate.htm for Gaussian output?"

[Robert Hanson]

Can't help you, sorry. But any of the applications at
https://chemapps.stolaf.edu/jmol/jsmol can do that. Take a look at
https://chemapps.stolaf.edu/jmol/jsmol/vibrate.htm.  It is a Spartan file
by default, but you should be able to drag drop a Gaussian output file into
it (although it may or may not automatically show vibration info).
Unfortunately I do not seem to have any Gaussian files that have IR data.





On Mon, Apr 3, 2017 at 1:24 PM, PASCAL Andrew  wrote:

> Hi
>
> I was looking into making a jsmol applet to read a Gaussian log file, and
> animate the vibrations it contains. I came across this old mailing list
> thread, but I don't know how to get it to my Email client to reply to it!
> (I'm newly-subscribed to the list):
>
> https://sourceforge.net/p/jmol/mailman/message/31853145/
>
> Would Matt Kubasik (or anyone else who may have done this) be prepared to
> share this jsmolvib.html? (Its no longer on the server referred to.)
>
> Thanks...
>
> andy pascal (andrew.pas...@cea.fr)
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>



-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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[Jmol-users] Jmol 14.11.0 released

[Robert Hanson]

Note that our numbering system now clicks higher in the second number every
time there is a new feature. The third number just indicates bug fixes. In
this case, the new features have to do with nucleic acids -- abilities to
color them using new schemes and also a new option "backboneBlocks" that
renders nucleic acids as abstract blocks similar to what DSSR can do
natively.

Bob

* Download Jmol-14.11.0-binary.zip (70.0 MB)
 *

Jmol.___JmolVersion="14.11.0" // released 4/1/2017

new feature: color NUCLEIC
 -- for nucleic only (others will be grey)
 -- based on DSSR nucleic color scheme:
  G green, C yellow, A red, T blue, U cyan

new feature: set backboneBlocks; set backboneBlockHeight x.x
 -- for nucleic only
 -- overrides set backboneSteps
 -- uses DSSR data if present (using calculate structure DSSR or load
=/dssr)
 -- displays a DSSR block for each base based on dssr.nts.frame
 -- x.x is height of box in Angstroms (default 0.5)

new feature: color property DSSR type
 -- where type is one of:
bulges
coaxStacks
hairpins
hbonds
helicies
iloops
isoCanonPairs
junctions
kissingLoops
multiplets
nonStack
nts
pairs
ssSegments
stacks
stems
 -- color is based on index into the list of the given structures
 -- 0 (not of that structure), 1 (first entry), 2 (second entry), etc.
 -- for example:

load =4fe5/dssr
backbone -0.5;set backboneSteps;
color property dssr junctions
color {color=red} grey   // just making "not this type" grey
instead of red

[ most bases are grey, but one region is green and one region is blue ]


bug fix: drag-drop of PDB file with isolated nucleic acids gives odd
unbonded look
bug fix: set drawPicking TRUE does not report pending measurement
bug fix: DSSR calculation should reset after atom coordinate changes
bug fix: using Jmol.scriptWait() within a callback will not work, as it
will overwrite the currently running eval object



-- 
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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engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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[Jmol-users] atom numbers different between PDB and CIF

[Robert Hanson]

Just a comment.

I was just reminded that atom numbers are different in PDB and CIF files.
For example,

load =1d66.pdb

ATOM387  C4   DG D  19  32.213  11.729  27.819  1.00
25.75   C
TER 388   DG D
19
ATOM389  O5'  DC E  20  20.466  11.694  21.639  1.00
40.14   O


load =1d66.cif

ATOM   387  C  C4. DG  A 1 19 ? 32.213 11.729 27.819 1.00 25.75
ATOM   388  O  "O5'" . DC  B 2 1  ? 20.466 11.694 21.639 1.00 40.14

I recommend starting to be explicit in your scripts as to which form you
want, PDB or CIF:

load =1d66.pdb
load =1d66.cif

Note that from EBI (PDBe), CIF is the default option. PDB format is not an
option there.

load *1d66




-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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[Jmol-users] ACS National Meeting call for papers

[Robert Hanson]

I would like anyone on this list who utilizes NCI/CADD or PubChem to
consider representing the Jmol community and making a presentation in this
symposium at the upcoming Fall ACS National Meeting to be held in
Washington, D.C., August 20-24, 2017.  Deadline for abstract submission is
April 10.

I, unfortunately, cannot make it, as I am making a presentation at the IUCr
Congress meeting in Hyderabad at exactly that time.

https://callforpapers.acs.org/dc2017/CINF

Symposium:  Government(-Funded) Chemical Databases & Open Chemistry

Description:  Governments, including the federal government of the United
States, develop and fund many chemical databases. They represent a
cornerstone of scientific infrastructure that, if not available, would
dramatically slow the rate of scientific discovery. This symposium will
explore the various government (funded) chemical databases and related open
chemistry technologies we, as a chemical community, depend on for
information.




-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Compare SMILES Question

[Robert Hanson]

Yes, I think that is appropriate.

$ print "C1=CC=CC=C1".find("smiles", "c1c1")
6
$ print "C1=CC=CC=C1".find("smiles", "/aromaticdefined/c1c1")
0

The first allows for different types of aromatic descriptions to be
matched; the second does not.

These "directives" are described in Table 8 of
https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0160-4



​
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Re: [Jmol-users] Jmol Keyboard Interaction

[Robert Hanson]

On Wed, Mar 29, 2017 at 2:14 PM, David Hibbitts  wrote:

> Thanks for the input everyone. The keyboard input will control jmol/jsmol
> but also do other things, but I do like using arrow keys to rotate the
> structure, for example. Other features can be added later to allow jmol to
> more easily *modify* rather than merely view structures. It's hard to
> imagine these features without a fuller keyboard interface (features
> similar to the structure-editing capabilities of avogadro or materials
> studio).
>

set modelkitmode

allows substantial editing, but perhaps not up to those programs in terms
of interface. Still, you can do a lot. Have you experimented with it?



>
> The javascript version already works perfectly, as keyed events are
> captured by the website (even if jsmol previously has focus) and I'm just
> using javascript to do whatever I want to do (including interacting with
> jsmol via JmolScript calls).
>
> For the java version, the best I've been able to do is: use a function
> which restores focus to the website (so they keyboard commands aren't
> trapped by jmol) whenever 1) a script is executed by jmol using
> ScriptCallback or 2) the users mouse leaves the jmol div (using a
> standard mouseout event in the DOM). This means the user doesn't have to
> "click" off of jmol to restore focus and re-enable the keyboard
> interactions. It doesn't help if the user, for example, uses the mouse to
> rotate the structure and leaves the mouse on jmol the entire time. In
> that instance, jmolnever loses focus and so the keyboard events aren't
> passed to the website.
>

That's clever.


>
> I could use the callbacks more aggressively, for example by using
> pickcallback and hovercallback -- but those are uncommon cases -- what I
> really need is something more encompassing like a "MouseUpCallback" so that
> any time the clicks on jmol I can redirect focus back to the website.
> Unfortunately, that callback doesn't exist in the jmol scripting
> environment.
>
>

> It's hard to know how much any of us should invest in these java-specific
> issues given the aggressive nature of browsers toward javascript -- but my
> website really serves my research group, not the general public, and there
> I can certainly get the users to install Waterfox+JAVA.
>
>
Ah, that is very good to hear. I have been trying to promote the idea that
browser-based Jmol can be very much for local use such as that.

Bob
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Re: [Jmol-users] Jmol Keyboard Interaction

[Robert Hanson]

(sorry, I missed that nuance)
​
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Re: [Jmol-users] Jmol Keyboard Interaction

[Robert Hanson]

Only the JavaScript version.

On Wed, Mar 29, 2017 at 11:32 AM, Rolf Huehne <rolf.hue...@leibniz-fli.de>
wrote:

> Am 29.03.17 um 18:21 schrieb Robert Hanson:
> > David,
> >
> > OK, so the beauty of this system is that you can implement any sort of
> > additional functionality you want using readily available methods that
> > have nothing to do with Jmol or JSmol. It's one of the bonuses of
> > working in JavaScript and jQuery.
> >
> > So, for example, if you want to implement a key listener that
> > implements  + and - to actuate zooming, you can do it this way:
> >
> > c = $("#jmolApplet0_canvas2d")
> > c.attr("tabindex", 1)
> > c.mouseover(function(){c.focus()})
> > c.keypress(function(e){
> >   if (e.key == "+")Jmol.script(jmolApplet0, "zoom *1.2")
> >   else  if (e.key == "-")Jmol.script(jmolApplet0, "zoom /1.2")
> > })
> >
> > Notice that to accept key events, we must (a) provide a tabindex to the
> > canvas and (b) make sure the canvas has focus when we are looking for
> > key events.
> >
> > I would only say that hidden specialized features like this, though
> > potentially useful, are not necessarily recommended.
> > ​
> It looks like the example would only work for the Javascript version. Or
> could it also work for the Java version (with some adjustment)?
>
> Regards,
> Rolf
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>



-- 
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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Re: [Jmol-users] Jmol Keyboard Interaction

[Robert Hanson]

David,

OK, so the beauty of this system is that you can implement any sort of
additional functionality you want using readily available methods that have
nothing to do with Jmol or JSmol. It's one of the bonuses of working in
JavaScript and jQuery.

So, for example, if you want to implement a key listener that implements  +
and - to actuate zooming, you can do it this way:

c = $("#jmolApplet0_canvas2d")
c.attr("tabindex", 1)
c.mouseover(function(){c.focus()})
c.keypress(function(e){
  if (e.key == "+")Jmol.script(jmolApplet0, "zoom *1.2")
  else  if (e.key == "-")Jmol.script(jmolApplet0, "zoom /1.2")
})

Notice that to accept key events, we must (a) provide a tabindex to the
canvas and (b) make sure the canvas has focus when we are looking for key
events.

I would only say that hidden specialized features like this, though
potentially useful, are not necessarily recommended.
​

Bob
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[Jmol-users] Jmol 14.10.0 released

[Robert Hanson]

major new capabilities include:

Using SMARTS and a new .find() option to select and create polyhedra based
on ring size criteria.

An extension of the MOL file format to allow 4-, 5-, and 6-order bonds
along with the capability to render those high-order bonds.

see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.10/Jmol%2014.10.0/
https://sourceforge.net/projects/jmol/files/latest/download?source=files

Jmol.___JmolVersion="14.10.0" // released 3/25/2017

new feature: x = {*}.find(smartsString,"map")
 -- returns an array of arrays of atom indices (0-based)
 -- indicates exact correlation between atoms in {*} and atoms of
smartsString
 -- only unique sets of atoms are found, not every possibility
 -- for example:

  load $caffeine
  print {*}.find("*1*1", "map").format("JSON")

[ [ 0,2,4,6,11,12 ] ]

new feature: SELECT @x  where x is an array of integers or array of array
of integers
 -- selects atoms from array rather than from a bitset
 -- note that variable must be used, as SELECT [1,2,3] would look for PDB
group "1,2,3"
 -- for example:

  load $caffeine
  x = {*}.find("*1*1", "map")[0]
  select @x

6 atoms selected

new feature: DRAW polygon @face @points
 -- draws a filled polygon based on arrays of atom indices
 -- @face is an array of integers, not necessarily wound correctly
 -- @points is an atom bitset or an array of points (optional, defaults to
{*}
 -- for example:

   load $p4
  x = {*}.find("*1**1","map");
  draw ID p4r polygon @{x[1]} color red
  draw ID p4b polygon @{x[2]} color blue
  draw ID p4y polygon @{x[3]} color yellow
  draw ID p4g polygon @{x[4]} color green


new feature: DRAW polyhedron @faces @points
 -- draws sets of polygons based on arrays of atom indices
 -- @faces is an array of array of integers, not necessarily wound correctly
 -- @points is an atom bitset or an array of points (optional, defaults to
{*}
 -- for example:

load $caffeine
  draw polyhedron @{{*}.find("*11||*1*1","map")}

   load $p4
  draw ID p polyhedron @{{*}.find("*1**1","map")} color red

new feature: POLYHEDRON ID xxx @faces @points
 -- @faces is an array of array of integers, not necessarily wound correctly
 -- @points is an atom bitset or an array of points (optional, defaults to
{*}

load $p4
  polyhedra ID p4 @{{*}.find("*1**1","map")}

new feature: 4-order bond in MOL file using 14 for bond order
 -- Jmol extension for MOL file format to allow 4-bond
 -- example: [Re2Cl8](2-)
 -- see https://en.wikipedia.org/wiki/Quadruple_bond

new feature: 5-order bond in MOL file using 15 for bond order
 -- Jmol extension for MOL file format to allow 5-bond
 -- example: [Mo2Cl8](4-)
 -- see https://en.wikipedia.org/wiki/Quintuple_bond

new feature: 6-order bond in MOL file using 16 for bond order
 -- Jmol extension for MOL file format to allow 6-bond
 -- example: Mo2
 -- see https://en.wikipedia.org/wiki/Sextuple_bond

new feature: load "=/dssr--xxx=yyy"
 -- allows adding specialized options to dssr
 -- --xxx=yyy added on to = search item

bug fix: DSSR fix for multi-model PDB file
bug fix: DSSR - 4fe5 HPA ligand causes set backboneSteps true to fail
bug fix: EXIT command with -n command line flag does not exit Jmol
bug fix: echo renderer may not show correct font size
bug fix: POLYHEDRA ID id OFFSET {x y z} broken
bug fix: ScriptManager debug output being sent even if -i (silent) command
line option set.



Bob


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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https://lists.sourceforge.net/lists/listinfo/jmol-users