[Jmol-users] [n = {*}[0].molecule;show n] bug

[Otis Rothenberger]

Bob,

First, AAARGH! Finally.

Here’s what messes up [n = {*}[0].molecule;show n] in Jmol - Otis.htm and 
Test2.htm

PubChem provides SDF's with partial charges and without partial charges. 
Actually, they are always there, but some are listed

 > 
0

If the PubChem file actually lists non-zero charges, then cutting the resulting 
molecule up in Jmol makes  [n = {*}[0].molecule;show n]  behave erratically.

I load by default from PubChem, and a McLafferty Rearrangement model kit 
problem using hexanal that I was setting up started this whole email chain with 
the mf problems. I just kept working with PubChem hexanal while I was trying to 
find the “funky” behavior on my page. It was just dumb luck that I noticed the 
PubChem relationship.

OK, now that I can use n = {*}[0].molecule, I need to get the mf array over to 
JavaScript. What’s the best route - message callback?

Finally, it seems to me that if CH2 is in the Jmol window, then a simple 
extraction of mf should be CH2 - not CH4. I’m just saying. This, of course, is 
a small molecule guy’s opinion!

Otis

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


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Re: [Jmol-users] RCSB

[Robert Hanson]

Ouch!!

On Tue, Jun 28, 2016 at 4:49 PM, Otis Rothenberger 
wrote:

> Phil,
>
> In my attempt to locate my [n={*}[0].molecule;show n] problem mentioned in
> a previous email, I downloaded today’s version. I can confirm pdb load
> problem. The console says the pdb is loaded, but nothing is visible.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> > On Jun 28, 2016, at 8:53 AM, Philip Bays  wrote:
> >
> > In today’s version (…..6.28) the RCSB protein files in jsmol.htm do not
> load correctly.  Yesterday’s version (….6.27)  worked.  Can anyone else
> confirm that?
> >
> > Phil
> >
> >
> > Philip Bays
> > Emeritus Professor of Chemistry
> > Saint Mary's College
> > Notre Dame, IN 46556
> > pb...@saintmarys.edu
> >
> >
> >
> >
> --
> > Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> > Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> > present their vision of the future. This family event has something for
> > everyone, including kids. Get more information and register today.
> > http://sdm.link/attshape
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
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> 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] page-developer request - Jmol Unplugged

[Otis Rothenberger]

Bob,

For the past year, I have working to make the model kit self contained. To do 
this, I am detecting 3 states:

1) On-line and served.
2) On-line and local.
3) Local only.

The code automatically detects these states and does 3 things (item numbers 
below ref above item numbers):

1) Good to go - have fun.

2) Good to go - have fun.

3) Shift to alternate approach or put up off-line notice - e.g. 2D JME to 3D 
Jmol auto switches to direct Jmol load of JME (no notice) OR PubChem contact 
attempt (off line notice).

My plan is to give this all to Delmar at BCCE for ChemWiki. Local running is 
also a component of my BCCE presentation. My plan all along was to give this 
thing to folks who want it, so that fits in well with your suggested approach.

Otis 

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

> On Jun 28, 2016, at 9:00 AM, Robert Hanson  wrote:
> 
> Jmol page developers,
> 
> Today I am giving a workshop on the use of Jmol in general and inorganic 
> chemistry. Tomorrow the subject is organic chemistry, and Thursday it is 
> physical chemistry. These workshops are at the Universidad Mayor San Simón, 
> in Cochabama, Bolivia. Please feel free to come and help me out!
> 
> While there is widespread fast internet in Bolivia, there are certainly times 
> and places where it is not available. (One of those places is an auditorium 
> where I am giving another presentation tomorrow.)
> 
> I have an idea that will change the way Jmol is used in many parts of the 
> world. It will open up opportunities for millions of students and thousands 
> of professors and high-school teachers to use Jmol. It's simple. I'm not sure 
> exactly what to call it, but for now I am calling it "Jmol Unplugged". Here 
> is the idea:
> 
> Somewhere - possibly SourceForge - we create a site where people can upload 
> fully contained web site "packages" that amount to stand-alone web 
> applications. For example, I just created this directory:
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites 
> 
> 
> where we find
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/coolMolecules.zip 
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/orbitals.zip 
> 
> 
> These are the fully-contained fully operational JavaScript versions of 
> 
> http://www.stolaf.edu/depts/chemistry/mo/struc 
>  
> http://chemapps.stolaf.edu/jmol/orbitals 
>  
> 
> They can be downloaded to a laptop and -- provided the browser is set up for 
> local file reading -- they will run totally disconnected from the web.
> 
> The conditions for curation would be something like this:
> 
> 1)  For the most part the site must work without an internet connection. It 
> would be fine if it still has a few links to external pages that are not 
> critical to the function of the site. But the primary function of the site 
> would have to be self-contained. That means no use of NCI Resolver, PubChem, 
> or RCSB, for example.
> 
> 2) The site is JavaScript only. Or, at least it is either Java-only or 
> JS-only, and if it is Java only, that is clearly indicated in its file name. 
> 
> 3) The contributor understands that they are giving away their site. Someone 
> can now take it, change it, put it up somewhere on their own. Whatever. Maybe 
> there's a licensing agreement that has to be worked out. I don't know.
> 
> Obviously we would  need some sort of introductory page with descriptions of 
> the site packages. I think that would be a Wiki -- maybe even Wikipedia? Not 
> sure about that. 
> 
> We would have to think about whether we want to have these totally 
> self-contained, with the  j2s directory, or not. My inclination is that we DO 
> have them contain the j2s directory so that no changes to Jmol affect the 
> site. But there might be other options there. I don't want to make this more 
> complicated than it has to be.
> 
> I think there's a publication in this for anyone who wants to help organize 
> it and get it off the ground. It will take some effort to standardize it, 
> figure it out, and curate it.
> 
> Right now I am asking for anyone who wants to contribute their work to send 
> me a link to a zip file that, when opened, contains your site and fits these 
> criteria. 
> 
> If you would let me use your site in my workshops and put them up temporarily 
> at chemapps.stolaf.edu , send me a link today.
> 
> Thank you!
> 
> 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 

Re: [Jmol-users] page-developer request - Jmol Unplugged

[J. Bays]

Bob:
Here is a link to a directory that contains stereochemistry and spectroscopy 
tutorials which our students have found helpful.  It is small and runs without 
network connection.  The index file contains the links to the two sets of 
tutorials, or you can just open them from the appropriately titled .htm files.

https://dl.dropboxusercontent.com/u/17514932/PBays.zip 



> On Jun 28, 2016, at 9:00 AM, Robert Hanson  wrote:
> 
> Jmol page developers,
> 
> Today I am giving a workshop on the use of Jmol in general and inorganic 
> chemistry. Tomorrow the subject is organic chemistry, and Thursday it is 
> physical chemistry. These workshops are at the Universidad Mayor San Simón, 
> in Cochabama, Bolivia. Please feel free to come and help me out!
> 
> While there is widespread fast internet in Bolivia, there are certainly times 
> and places where it is not available. (One of those places is an auditorium 
> where I am giving another presentation tomorrow.)
> 
> I have an idea that will change the way Jmol is used in many parts of the 
> world. It will open up opportunities for millions of students and thousands 
> of professors and high-school teachers to use Jmol. It's simple. I'm not sure 
> exactly what to call it, but for now I am calling it "Jmol Unplugged". Here 
> is the idea:
> 
> Somewhere - possibly SourceForge - we create a site where people can upload 
> fully contained web site "packages" that amount to stand-alone web 
> applications. For example, I just created this directory:
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites 
> 
> 
> where we find
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/coolMolecules.zip 
> 
> http://chemapps.stolaf.edu/jmol/unplugged/sites/orbitals.zip 
> 
> 
> These are the fully-contained fully operational JavaScript versions of 
> 
> http://www.stolaf.edu/depts/chemistry/mo/struc 
>  
> http://chemapps.stolaf.edu/jmol/orbitals 
>  
> 
> They can be downloaded to a laptop and -- provided the browser is set up for 
> local file reading -- they will run totally disconnected from the web.
> 
> The conditions for curation would be something like this:
> 
> 1)  For the most part the site must work without an internet connection. It 
> would be fine if it still has a few links to external pages that are not 
> critical to the function of the site. But the primary function of the site 
> would have to be self-contained. That means no use of NCI Resolver, PubChem, 
> or RCSB, for example.
> 
> 2) The site is JavaScript only. Or, at least it is either Java-only or 
> JS-only, and if it is Java only, that is clearly indicated in its file name. 
> 
> 3) The contributor understands that they are giving away their site. Someone 
> can now take it, change it, put it up somewhere on their own. Whatever. Maybe 
> there's a licensing agreement that has to be worked out. I don't know.
> 
> Obviously we would  need some sort of introductory page with descriptions of 
> the site packages. I think that would be a Wiki -- maybe even Wikipedia? Not 
> sure about that. 
> 
> We would have to think about whether we want to have these totally 
> self-contained, with the  j2s directory, or not. My inclination is that we DO 
> have them contain the j2s directory so that no changes to Jmol affect the 
> site. But there might be other options there. I don't want to make this more 
> complicated than it has to be.
> 
> I think there's a publication in this for anyone who wants to help organize 
> it and get it off the ground. It will take some effort to standardize it, 
> figure it out, and curate it.
> 
> Right now I am asking for anyone who wants to contribute their work to send 
> me a link to a zip file that, when opened, contains your site and fits these 
> criteria. 
> 
> If you would let me use your site in my workshops and put them up temporarily 
> at chemapps.stolaf.edu , send me a link today.
> 
> Thank you!
> 
> 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
> 
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information 

Re: [Jmol-users] RCSB

[Otis Rothenberger]

Phil,

In my attempt to locate my [n={*}[0].molecule;show n] problem mentioned in a 
previous email, I downloaded today’s version. I can confirm pdb load problem. 
The console says the pdb is loaded, but nothing is visible.

Otis

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

> On Jun 28, 2016, at 8:53 AM, Philip Bays  wrote:
> 
> In today’s version (…..6.28) the RCSB protein files in jsmol.htm do not load 
> correctly.  Yesterday’s version (….6.27)  worked.  Can anyone else confirm 
> that?
> 
> Phil
> 
> 
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


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Re: [Jmol-users] page-developer request - Jmol Unplugged

[Angel Herráez]

Dear Bob

I will likely  get involved on this.
For now, just two quick comments that popped up:

1. 
I have had big trouble running my pages locally since I moved to JSmol. That 
may be due to them being old and ellaborate, with a combination of folders, 
pdb or mol files, scripts, common JS files... across folders that I've never 
been able to figure out which is the key of the problem. I just gave up and 
resort to either online or local webserver when needed --not that I am happy 
with that
So any contribution from my side will need reserach and possibly relocation


2. 
Proteopedia has a similar feature in the sense that any Poteopedia page can 
be packed for download and should run offline - the download includes all 
components including JSmol and j2s files -- This can be a reference for 
hosting or methods of delivery.

3.
Giving away:  Creative Commons licences do a decent job at that - you can 
pick the conditions you prefer for sharing



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Re: [Jmol-users] resolution of JPG images

[Angel Herráez]

Hi Rick
a few comments:

1. I can recommend that you try PovRay output. It is PNG, transparent 
background and much better look. You don't need to learn how to use 
PovRay, producing the images is straightforward. You have to install 
PovRay, export to PovRay format from Jmol and then save from PovRay to 
PNG

2. I do not think that JPG may have transparent bacground; it would be white 
maybe. And as Bob says, the quality is always worse -- the only advantage is 
smaller files, at the cost of quality loss.

3. Given the way Jmol works for rendering I believe a vector format is not 
possible. VRML is possibly the closest to that idea, as it is made of 
"objects", 
but it is not practical for image production.

Do try PovRay with eg 1000 px size, you will be surprised!

I have a not particularly brilliant example at 
http://biomodel.uah.es/Jmol/export-image/exportPNG/



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[Jmol-users] RCSB

[Philip Bays]

In today’s version (…..6.28) the RCSB protein files in jsmol.htm do not load 
correctly.  Yesterday’s version (….6.27)  worked.  Can anyone else confirm that?

Phil


Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



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Re: [Jmol-users] resolution of JPG images

[Robert Hanson]

Rick, the first thing you should do is contact your publisher and make
absolutely certain they cannot accept PNG images. In all cases PNG images
are better than JPG because they are "lossless". JPG images notoriously
have artifact pixels that are not part of the actual image. I don't think
the 72-ppi business should be any issue. There are any number of image
processing tools that let you convert one image to any sort of other image.
PNG->JPG, PNG->TIFF. Your publisher has them, I have them.

Bob
​
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Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

[Robert Hanson]

Otis, this is because your site is doing something funky. Or there's a bug.

{*}[0] is an atom reference, not a number. It has all the properties of an
atom, including .molecule.


​
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[Jmol-users] page-developer request - Jmol Unplugged

[Robert Hanson]

Jmol page developers,

Today I am giving a workshop on the use of Jmol in general and inorganic
chemistry. Tomorrow the subject is organic chemistry, and Thursday it is
physical chemistry. These workshops are at the Universidad Mayor San Simón,
in Cochabama, Bolivia. Please feel free to come and help me out!

While there is widespread fast internet in Bolivia, there are certainly
times and places where it is not available. (One of those places is an
auditorium where I am giving another presentation tomorrow.)

I have an idea that will change the way Jmol is used in many parts of the
world. It will open up opportunities for millions of students and thousands
of professors and high-school teachers to use Jmol. It's simple. I'm not
sure exactly what to call it, but for now I am calling it "Jmol Unplugged".
Here is the idea:

Somewhere - possibly SourceForge - we create a site where people can upload
fully contained web site "packages" that amount to stand-alone web
applications. For example, I just created this directory:

http://chemapps.stolaf.edu/jmol/unplugged/sites

where we find

http://chemapps.stolaf.edu/jmol/unplugged/sites/coolMolecules.zip
http://chemapps.stolaf.edu/jmol/unplugged/sites/orbitals.zip

These are the fully-contained fully operational JavaScript versions of

http://www.stolaf.edu/depts/chemistry/mo/struc
http://chemapps.stolaf.edu/jmol/orbitals

They can be downloaded to a laptop and -- provided the browser is set up
for local file reading -- they will run totally disconnected from the web.

The conditions for curation would be something like this:

1)  *For the most part* the site must work without an internet connection.
It would be fine if it still has a few links to external pages that are not
critical to the function of the site. But the primary function of the site
would have to be self-contained. That means no use of NCI Resolver,
PubChem, or RCSB, for example.

2) The site is JavaScript only. Or, at least it is either Java-only or
JS-only, and if it is Java only, that is clearly indicated in its file
name.

3) The contributor understands that they are giving away their site.
Someone can now take it, change it, put it up somewhere on their own.
Whatever. Maybe there's a licensing agreement that has to be worked out. I
don't know.

Obviously we would  need some sort of introductory page with descriptions
of the site packages. I think that would be a Wiki -- maybe even Wikipedia?
Not sure about that.

We would have to think about whether we want to have these totally
self-contained, with the  j2s directory, or not. My inclination is that we
DO have them contain the j2s directory so that no changes to Jmol affect
the site. But there might be other options there. I don't want to make this
more complicated than it has to be.

I think there's a publication in this for anyone who wants to help organize
it and get it off the ground. It will take some effort to standardize it,
figure it out, and curate it.

Right now I am asking for anyone who wants to contribute their work to send
me a link to a zip file that, when opened, contains your site and fits
these criteria.

If you would let me use your site in my workshops and put them up
temporarily at chemapps.stolaf.edu, send me a link today.

Thank you!

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
--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
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Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

[Otis Rothenberger]

Bob,

> 
> {*}[0]  
> 

Agree: It appears to generate the atomIndex of the last atom.

> {*}[0].molecule
> 

I don’t think so: It consistently generates the number 1 for any number of 
fragments in the window.

On the other hand, using the infinite number of monkeys writing Shakespeare 
approach, n = {*}[-1].molecule generates the number of models! Go figure…

Otis--
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[Jmol-users] resolution of JPG images

[Spinney, Richard]

I am trying to produce some high quality images for publication and would like 
to use JSmol, however it seems that the resolution is set at 72 dpi and cannot 
be changed. It is possible to make this a variable the user can set? Also (for 
the wish list) any chance of getting a vector format such as eps or svg 
working? Also transparent backgrounds for all image types not just the PNGT?

Thanks, Rick

Dr. Richard Spinney
Department of Chemistry & Biochemistry
The Ohio State University
120A Celeste Laboratory
120 West 18th Ave
Columbus, Ohio 43210

Email: 
rspin...@chemistry.ohio-state.edu
Phone:(614) 247 - 6847
Fax:  (614) 292 - 1685

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Re: [Jmol-users] Molecular Formula Problem Related to Breaking a Bond

[Robert Hanson]

On Tue, Jun 28, 2016 at 1:24 AM, Otis Rothenberger 
wrote:

> Bob,
>
> My model kit puts multiple models in the same Jmol frame. It appears that n
> = {*}.molecule[0] (not n = {*}[0].molecule) is the correct expression,
> but results are very erratic. The value of n is often (but not always) 2X
> the number of fragments, with the extra “mf” values = “”.
>
> I don't think so.

{*}[0]

means "the  last atom"

so

{*}[0].molecule

means "the number of molecules"


{*}.molecule

is a number, specifically the average molecule number for all atoms.

{*}.molecule[0]

converts that number to a string and takes the first digit.




-- 
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
--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Download Jmol-14.6.0_2016.06.28-binary.zip (66.5 MB)

[Robert Hanson]

Jmol.___JmolVersion="14.6.0_2016.06.28"

bug fix: using an exporter (write VRML, eg) with cartoonsFancy will break
rendering after that
bug fix: after loading PNGJ data, using write FILE crashes Jmol


* Download Jmol-14.6.0_2016.06.28-binary.zip (66.5 MB)
 *

-- 
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
--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users