from:"Paul Pillot"

Re: [Jmol-users] getting the applet ID

2017-06-29 Thread Paul PILLOT

It’s probably not recommended, but this may do the trick
Object.keys(Jmol._applets) ?

Paul

> Le 29-06-2017 à 14:58, Angel Herráez  a écrit :
> 
> Callbacks return as their first parameter the ID of the JSmol object (e.g. 
> "jmolApplet1")
> 
> I wonder if this ID could be retrieved directly from a script. I could not 
> find 
> anything e.g. among the readonly variables
> 
> Any hints are welcome
> 
> 
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Re: [Jmol-users] Jmol Anniversaries?

2017-06-08 Thread Paul PILLOT

Hi,
digging in sourceforge jmol-developers list, I found that Bob starts appearing 
as a recurring character in 2005 and secures the leading role in developping 
Jmol in mid 2006 after having exhausted Miguel with thousands of messages and 
commits. That was around Jmol v10.x
It looks like we missed the 10th anniversary celebration ;)
As for Jsmol, there was an article published in 2013 announcing its release 
(was issued some month after the initial Jsmol tour de force) : 
https://chemapps.stolaf.edu/jmol/2013_Hanson_Prilusky_IJC.pdf 


Paul

> Le 08-06-2017 à 11:09, Eric Martz  a écrit :
> 
> Hi Henry,
> I have a paragraph of Jmol history in footnote 1 here:
> 
> http://proteopedia.org/w/Jmol 
> Which leads to early history by searching for "jmol" at openscience.org:
> http://openscience.org/?s=jmol 
> Much of Jmol's command language was invented by Roger Sayle when he created 
> RasMol. Tim Maffet used Roger's public domain source code when he created the 
> browser plug-in MDL Chime, which was the best within-browser solution from 
> 1996 until Jmol superceded it ca. 2006. Thus, Chime included most of RasMol's 
> command language. Michael "Miguel" Howard, who I believe first adapted Jmol 
> to display macromolecules, incorporated the RasMol/Chime command language 
> into Jmol, facilitating the transitions of RasMol and Chime users to Jmol. Of 
> course Jmol's command language is now vastly larger and more powerful and 
> complex than the languages of RasMol & Chime. But the original RasMol 
> language is still a core subset.
> Although far from complete, quite a bit of pre-Jmol history is here, 
> including physical models and early computer graphics:
> 
> http://History.MolviZ.Org 
> -Eric
> On 6/7/17 2:28 AM, Rzepa, Henry S wrote:
>> Does anyone know the various anniversary dates?
>> 
>> 1. Jmol (was it really only released in 2001?  I thought it came about just 
>> a year or so after  Java itself was released in 1996?)
>> 2. JSmol (2014?)
>> 3. Bob’s own entry after Miguel handed on (??)
>> 
>> Is there a hall of fame, going back perchance to  Xmol (which started the 
>> bandwagon, + Rasmol as a separate fork?) and key timelines/contributors? The 
>> Jmol Wikipedia page is not that strong on the history).
>> 
>> Henry Rzepa, http://orcid.org/-0002-8635-8390 
>> 
>> 
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Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

2017-05-15 Thread Paul PILLOT

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/ 
<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 
<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 
> <mailto: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 
> > <mailto: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/>
> > http://biomodel.uah.es/en/DIY/comparison.htm 
> > <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 even if tuning is possible to some extent. This is 
why I took a look at the alternatives currently flourishing on the web which 
rely on WebGL to display the 3D scenes in the browser. None of them could be 
considered as a replacement to JSmol for my purposes, but I th

Re: [Jmol-users] how to parse JSON data within Jmol

2016-01-13 Thread Paul PILLOT


Le 13-01-2016 à 20:58, Paul PILLOT <paulpil...@gmail.com> a écrit :

Hi Eric,
rcsb implements a REST API that you can query through Ajax to get many answers 
to a lot of question.
Here is an example of code I designed to get informations from a PDB, such as 
the number and names of chains, the ligands, the related pubmed abstract, etc…
PDB rest web service returns XML documents that can be easily parsed with 
Jquery built in fonctions : find() to get the main node, attr() to get specific 
node attributes.
My internet access is very slow at the moment, so I am not able to check which 
are the nodes you are looking after, but I am convinced that you could find the 
answers to your questions through this very powerful and effective channel.
Paul

$.ajax({
url: "http://www.pdb.org/pdb/rest/describePDB 
<http://www.pdb.org/pdb/rest/describePDB>",
data: {
structureId: pdb
},
success: function(txt){
var $xml = $(txt);
var node = $xml.find("PDB");
if (node.length==0) {
alert(« Unknown PDB 
identifier",'reponsePdb','error');
return;
}
var pId = node.attr("pubmedId");
var titre = node.attr("title");
var authors = 
node.attr('citation_authors');
var txt = 'Titre '+titre+' ';
txt += 'Pubmed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve=PubMed=Abstract_uids='+pId+'
 
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve=PubMed=Abstract_uids='+pId+'>">'+pId+''
txt += ' Auteurs '+authors;
txt+= '';
$('#reponsePdb').append(txt);
$('#reponsePdb').append('');
$('#auteur').val(authors);

$('#codePdb').val(pdb).triggerHandler('change');


$('#reponsePdb').data('pdb',pdb).data('pubmed_article',pId).data('auteurs_article',authors).data('titre_article',titre);

$('#imagePdb').append("");


$.ajax({
url: 
"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi 
<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi>",
data: {
db: "pubmed",
id: pId,
retmode: "xml",
rettype: "abstract"
},
success: function(txt){
//console.log(txt);
var $xml = $(txt);
var txt = '';
var pmc = 
$xml.find("ArticleId[IdType='pmc']").text();
var volume = 
$xml.find("Volume").text();
var revue = 
$xml.find("Title").text();
var pages = 
$xml.find("MedlinePgn").text();
var annee = 
$xml.find("Year:first").text();
var doi = 
$xml.find("ArticleId[IdType='doi']").text();
var abstract = 
$xml.find("AbstractText").text();

txt += 'in '+revue+' '+annee+' n°'+volume+ ' p'+pages+' 
';
if (pmc.length>0) txt 
+= 'http://www.ncbi.nlm.nih.gov/pmc/articles/'+pmc+'/ 
<http://www.ncbi.nlm.nih

Re: [Jmol-users] labels and zshade

2016-01-05 Thread Paul PILLOT

They were not neither hidden nor faded out in a previous version. 
I have a webpage here : 
http://librairiedemolecules.education.fr/outils/adn/adn.htm 
<http://librairiedemolecules.education.fr/outils/adn/adn.htm> where under « 
Afficher les étiquettes » you can display labels and see how they were 
maintained visible. This is version 14.0.1_2013.12.04
This previous setting was important for my (young) students as it allowed them 
to see the complete sequence of the dna chains. With the autohiding on 
rotation, they have to position the model in a specific orientation to have 
access to this whole information.
I understand it could be an undesirable behaviour in a majority of cases, so 
the best option may be to have a setting for that (disable label auto hiding). 
Do you think it could be feasible ?
Thank-you
-Paul

> Le 04-01-2016 à 23:07, Robert Hanson <hans...@stolaf.edu> a écrit :
> 
> I believe that is the design. Otherwise labels would be faded out and 
> probably hard to read anyway. 
> 
> On Mon, Jan 4, 2016 at 8:45 PM, Paul PILLOT <paulpil...@gmail.com 
> <mailto:paulpil...@gmail.com>> wrote:
> Dear Jmolers,
> I don’t know if this is a recent change, but I’ve just realized with Jsmol 
> latest version that when zshade is on, labels of atoms located behind the mid 
> plane are hidden.
> Is there a way to switch off this behaviour ?
> -Paul
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> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
> 
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[Jmol-users] labels and zshade

2016-01-04 Thread Paul PILLOT

Dear Jmolers,
I don’t know if this is a recent change, but I’ve just realized with Jsmol 
latest version that when zshade is on, labels of atoms located behind the mid 
plane are hidden.
Is there a way to switch off this behaviour ?
-Paul
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Re: [Jmol-users] test please

2015-12-21 Thread Paul PILLOT

I’ve made quick tests in Safari console.
array.slice() works
Int32Array.slice doesn’t work, but ArrayBuffer.slice from the same typed array 
works.
Paul

> Le 21-12-2015 à 17:03, Robert Hanson  a écrit :
> 
> Thanks, that's what I needed to know. Looks like "array.slice" or at least 
> Int32Array.slice is not a function in Safari. Bummer for that, but it is a 
> very localized problem I can certainly get around, I think.
> 
> On Mon, Dec 21, 2015 at 5:40 AM, Rolf Huehne  > wrote:
> Am 21.12.15 um 04:08 schrieb Philip Bays:
> > Bob:
> > Then link to your site does not work with Safari on the Mac,  Works with
> > Firefox and Chrome.  When I launch the file test2.htm from the desktop,
> > it again works in Firefox and Chrome but not Safari.  In this case the
> > list of files loading is visible and the crash comes at the following:
> >
> >
> > TypeError: b.slice is not a function. (In 'b.slice(c, d)', 'b.slice' is
> > undefined)
> >
> On MacOS X 10.9.5 I observe the same:
>Firefox 42.0 does work
>Chrome 47.0 does work
>Safari 7.1.3 does not work
> 
> --- Error message in 'info' during page load 
> TypeError: undefined is not a function (evaluating 'b.slice(c,d)')
> -
> 
> On Linux there is also a problem:
>Firefox 42.0 does work
>Chromium 31.0 does not work
> 
> --- Error message in 'info' during page load 
> TypeError: Object # has no method 'slice'
> -
> 
> Regards,
> Rolf
> 
> 
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> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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 scripting speed in JSmol/HTML5

2015-12-18 Thread Paul PILLOT

Regarding strings, from what I experienced, getting a value from an array is a 
lot faster when the array is index based than when the array is associative 
(strings as indexes)
Don’t know if that applies to your case...
Paul

> Le 18-12-2015 à 15:15, Robert Hanson  a écrit :
> 
> (the copy is the same as System.arraycopy -- it only copies references for 
> objects, but it copies scalars such as integers and floats.)
> 
> On Fri, Dec 18, 2015 at 2:05 PM, Robert Hanson  > wrote:
> Oh, yes. .slice() copies all or part of an array.  
> 
> That's certainly a major improvement. Excellent. Jsmol is now using .slice() 
> exclusively when possible. 
> I suspect some of that fast processing time is due to this use.
> 
> This is the kind of deep optimization that really have an effect. Great!
> 
> How about strings? Any suggestions for boosting that hugely?
> 
> Bob
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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 scripting speed in JSmol/HTML5

2015-12-18 Thread Paul PILLOT

According to jsperf ( https://jsperf.com/string-concatenation/106 ) your syntax 
seems optimal.
 
> Le 18-12-2015 à 15:30, Robert Hanson  a écrit :
> 
> I was thinking of alternatives to 
> 
> s = "a" + "b" + "c" 
> 
> 


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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

2015-12-16 Thread Paul PILLOT

Hi Rolf,
my experience in this area is not JSmol related, but when I had to deal with 
big tables in javascript (for a multiple sequence alignment script, aligning 2 
sequences of 5000 signs, requires at least 1 table of 5000 rows and 5000 
columns), I noticed that :
- using integers only tables is fastest
- opting for one dimensional array instead of two dimensional didn’t make a 
noticeable difference
- using typed arrays in some cases improved significantly the performance ( see 
https://developer.mozilla.org/en/docs/Web/JavaScript/Typed_arrays 
 ). This was 
2 years ago, and the browsers’ engine landscape can be quickly moving...
When you parse your data from your TSV file, are the fields stored as text ?

My 2 cents,
Paul

> Le 16-12-2015 à 13:12, Rolf Huehne  a écrit :
> 
> Hi all,
> 
> I am looking for some speedup tips for Jmol scripting in JSmol/HTML5.
> 
> The speed difference between JSmol/Java and JSmol/HTML5 for graphical 
> operations like rotation and zooming seems to be about 10 times or less 
> in Firefox and Chrome (if you don't consider the recent rotation speed 
> problems in Chrome).
> 
> Unfortunately the difference for Jmol scripting seems to be much higher 
> in my experience: about 50-70 times.
> 
> If I load for example 3 TSV (tab separated value) format files with 
> overall about 34,000 lines, JSmol/Java needs about 26 seconds for 
> laoding and parsing the data and putting it into a multi-level hash 
> structure. JSmol/HTML5 needs about 1700 seconds instead.
> 
> I already tried to write the final data structure into a file with 
> 'write VAR ...' and read it in again as a script (after adding a proper 
> variable assignment) but this already took in Java endlessly (I stopped 
> waiting after more than an hour...).
> 
> Q: Does anyone have any other ideas that might speed up this process?
> 
> Regards,
> Rolf
> 
> 
> -- 
> 
> Rolf Huehne
> Postdoc
> 
> Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
> 
> Phone:   +49 3641 65 6205
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Re: [Jmol-users] Fwd: Chrome: rotation unusable in JSmol

2015-12-10 Thread Paul PILLOT

Dear Eric,
I’ve noticed the same problems, especially on older computers where each scene 
repaint can be perceived (white background flashing between each frame). One of 
my pages has other concerns related to javascript event listeners that make the 
whole experience even worse, by adding other calculations to the webpage on top 
of JSmol. My students noticed that firefox is better too.
I have a simpler webpage with only buttons for interactions that doesn’t have 
the same drawbacks (animations are quirky, but user interactions are 
satisfactory).

As this situation has been quite frustrating, I’ve decided to give WebGL a try 
using 3dmol.js. I am in the process of rewriting a single page application 
around a viewer, but it’s like reinventing the wheel as this library 
capabilities are far from being on par with JSmol and rely on a totally 
different mechanism of interaction (David Koes, its main developper, is very 
helpful in this process). Most Jsmol features lack form this library which 
focuses on rendering. I’ll see if it nonetheless could suit my teaching needs 
in biochemistry…

-Paul

> Le 10-12-2015 à 17:55, Eric Martz  a écrit :
> 
> In April 2014, Chrome gave the best performance of JSmol: smoothest rotation 
> and few if any long (~ one minute) pauses during loading of some modest PDB 
> files (pauses seen in Firefox). I configured FirstGlance in Jmol, when using 
> JSmol, to recommend Chrome over Firefox. Safari was good. Internet Explorer 
> was unusably slow with JSmol.
> 
> Recently I began to notice jumpier rotation in Chrome, while Firefox and 
> Safari continue to perform well.
> 
> Today I found Chrome to be unable to rotate any molecule (even caffeine) in 
> JSmol. Although there are brief moments when rotation can be seen, these are 
> broken by long freezes (> 5 sec) when no rotation can be accomplished.
> 
> The problem is worst when the mouse is moved quickly. The molecule freezes 
> until the mouse is stopped. If you keep moving the mouse, the molecule may 
> freeze for more than 10 sec. The molecule does rotate with very slow 
> movements of the mouse.
> 
> The problem occurs in OS X, where Chrome has updated to version 47.
> 
> Rotation is still quite good in Chrome version 46, which happens to remain in 
> my Windows 7 and 10 machines, despite version 47 becoming the stable release 
> on December 1 ( 
> http://googlechromereleases.blogspot.com/search?updated-max=2015-12-01T12:43:00-08:00=10
>  
> ).
>  Presumably my Windows Chrome will shortly auto-update to 47 and then I will 
> be very curious about performance.
> 
> I tested the OS X beta version of Chrome, version 48, in hopes the problem 
> would be fixed -- but it remains in Chrome 48 in OS X.
> 
> Since Chrome stopped supporting Java on September 1, 2015, Chrome is now 
> useless for JSmol websites.
> 
> We can hope this is a mouse-related bug in Chrome that will be fixed, but as 
> I mentioned, a fix is not present in the current beta version 48.
> 
> This is a sad turn of events! Comments? Suggestions? Insights?
> 
> -Eric
> 
> 
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Re: [Jmol-users] draw curved arrows

2015-11-16 Thread Paul PILLOT

Angel & Killian,
"set hermitelevel 7" would be more appropriate when using povray for an output
(antialias doesn’t change the geometries in the pov file)
Paul

> Le 16-11-2015 à 12:14, Angel Herráez  a écrit :
> 
> Hi Kilian 
> 
> I'm afraid the succession of spheres is Jmol's only way of producing curved 
> lines (also used for protein cartoons and traces)
> 
> Have you tried adjusting set antiAliasDisplay ?
> 
> 
> Baerwinkel escribió:
> 
>> Hi fellow Jmolers!
>> 
>> I am preparing some structure plots with Jmol and PovRay, and I must say 
>> Jmol does an overall splendid job there. 
>> 
>> I have one question left before perfection:
>> 
>> Is it possible to draw a curved arrow with a smooth surface? As far as i can 
>> see, "draw arrow arc" as well as "draw arrow ..." with a sufficient number 
>> of points supplied yield a nicely curved arrow, but they both draw it via a 
>> chain of spheres. Unfortunately, this looks a bit poor in high-resolution 
>> pictures... 
>> 
>> Any suggestions?
>> 
>> Best
>> 
>> Kilian
>> 
>> P.S.: If this is at all impossible, I will just add these arrows in an 
>> external program, but I quite like the fact that it is possible to prepare 
>> publication-ready pictures with just Jmol -> adjust resolution/shadows in 
>> textfile -> povray.
>> 
>> 
>> __
>> 
>> Kilian Bärwinkel, M.Sc.
>> 
>> Lehrstuhl für Anorganische Chemie III
>> Gebäude NW 1 
>> Universität Bayreuth 
>> Universitätsstr. 30 
>> 95447 Bayreuth 
>> 
>> Tel:+49 921 55 - 3653
>> Fax:+49 921 55 - 2788 
>> 
>> e-mail: kilian.baerwin...@uni-bayreuth.de
>> 
>> http://www.senker.uni-bayreuth.de
>> 
>> 
>> --
>> Presto, an open source distributed SQL query engine for big data, initially
>> developed by Facebook, enables you to easily query your data on Hadoop in a 
>> more interactive manner. Teradata is also now providing full enterprise
>> support for Presto. Download a free open source copy now.
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> 
> 
> 
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> developed by Facebook, enables you to easily query your data on Hadoop in a 
> more interactive manner. Teradata is also now providing full enterprise
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Re: [Jmol-users] set picking rotate bond broken ?

2015-11-12 Thread Paul PILLOT

Otis,
what Bob means is that the command « set picking rotatebond » by itself is not 
broken. But it requires a key modifier + mouse drag combination to work. What I 
did on my webpage (thanks to the code I saw on yours) is to as a bind command 
as previously explained, so that no key modifier is required.
Paul

> Le 12-11-2015 à 16:14, Otis Rothenberger  a écrit :
> 
> Bob,
> 
> I’m not seeing what your note suggests on Paul’s page. No modifier key is 
> required from what I’m seeing. You give up model translation by doing this, 
> but the point is to make it work on a touch pad. By unbinding default 
> left-click and binding it to bond rotation, only click (or touch) drag is 
> required to rotate the bond.
> 
> On my page, I try to make up for this with two buttons - Rotate Bond and 
> Move. Between these two buttons, you have complete control of translate, 
> rotate, and bond rotate without the use of modifier keys:
> 
> http://chemagic.com/molecules/mini.html
> 
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
>> On Nov 12, 2015, at 3:55 PM, Robert Hanson  wrote:
>> 
>> It's working. But how it works is less than obvious. After clicking on a 
>> bond such that the two highlighted atoms stay highlighted, move off past the 
>> end you want to rotate, press SHIFT, and drag.
>> 
>> --
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> 
> 
> 
> 
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Re: [Jmol-users] set picking rotate bond broken ?

2015-11-12 Thread Paul PILLOT

Thank-you for the pointer.
I think we have two different implementations. From what I can guess from your 
webpage, once the user clicks a bond, the scripts somehow selects one of the 
group from either side of the bond to allow it to rotate (an « allow 
rotateselected » flag is set in the console).
In my webpage ( 
http://librairiedemolecules.education.fr/outils/scribmol/scrib.html excuse my 
french), upon clicking the 9th button on top of the jsmol window, a «  set 
picking rotatebond; bind ‘LEFT+drag’ _rotateBranch » command is issued. after 
clicking on a bond, red circles are displayed around the atoms defining the 
bond, and when the user drags the mouse, the group located on the side of the 
screen delimited by the bond, rotates. It is still possible to rotate the 
entire model, by clicking elsewhere (not on a bond) on the screen (I suspect 
it’s what you meant by frozen molecule).
Paul

> Le 12-11-2015 à 00:58, Otis Rothenberger <osrot...@chemagic.com> a écrit :
> 
> Paul,
> 
> Don’t forget that when you do that, you’ll be freezing the model. I decided 
> that I could live with that for my purposes:
> 
> http://chemagic.com/molecules/mini.html
> 
> Click the Rotate Bond button.
> 
> With multiple models in the window, the combination of  the  Rotate Bond 
> button and the Move button give me complete control of all model motions 
> (rotate, bond-rotate, translate) for the individual molecules. I must accept 
> a frozen molecule during the bond rotation, however.
> 
> You probably know this, but it took me a while to understand this point even 
> though it’s clearly stated in the docs: the unbind command by itself returns 
> to Jmol default bindings.
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
>> On Nov 11, 2015, at 10:03 PM, Paul PILLOT <paulpil...@gmail.com> wrote:
>> 
>> Thanks Otis !
>> your answer pointed me to a description of the gesture I was looking for : 
>> MAJ+Left_click
>> I’ll follow your lead and change the combination to a simple click so that 
>> touch screen users could use this feature.
>> Paul
>> 
>>> Le 11-11-2015 à 20:39, CheMagic <osrot...@chemagic.com> a écrit :
>>> 
>>> Paul,
>>> 
>>> I do this type of rotation by another method because I want it to work on a 
>>> touch screen, so I may be wrong on this point (below) with the set picking 
>>> rotatebond:
>>> 
>>> I think you still have to make the binding using the bind command. Are you 
>>> using the bind command to bind to a specific mouse/key action?
>>> 
>>> Otis
>>> 
>>> Sent from my iPad
>>> 
>>>> On Nov 11, 2015, at 8:06 PM, Paul PILLOT <paulpil...@gmail.com> wrote:
>>>> 
>>>> Hi,
>>>> I am wondering if the « set picking rotatebond » command is broken ? I’ve 
>>>> tried bot with the application (v 14.5.0_2015.11.06) and the HTML5 jsmol 
>>>> flavour
>>>> Bonds are selected by picking, but I can’t rotate any group from either 
>>>> side of the bond. Am I missing something (key modifier for example ?)
>>>> Thanks for your help,
>>>> Paul
>>>> --
>>>> ___
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>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> 
>>> 
>>> 
>>> --
>>> ___
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>> 
>> 
>> --
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> 
> 
> 
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Re: [Jmol-users] set picking rotate bond broken ?

2015-11-11 Thread Paul PILLOT

Thanks Otis !
your answer pointed me to a description of the gesture I was looking for : 
MAJ+Left_click
I’ll follow your lead and change the combination to a simple click so that 
touch screen users could use this feature.
Paul

> Le 11-11-2015 à 20:39, CheMagic <osrot...@chemagic.com> a écrit :
> 
> Paul,
> 
> I do this type of rotation by another method because I want it to work on a 
> touch screen, so I may be wrong on this point (below) with the set picking 
> rotatebond:
> 
> I think you still have to make the binding using the bind command. Are you 
> using the bind command to bind to a specific mouse/key action?
> 
> Otis
> 
> Sent from my iPad
> 
>> On Nov 11, 2015, at 8:06 PM, Paul PILLOT <paulpil...@gmail.com> wrote:
>> 
>> Hi,
>> I am wondering if the « set picking rotatebond » command is broken ? I’ve 
>> tried bot with the application (v 14.5.0_2015.11.06) and the HTML5 jsmol 
>> flavour
>> Bonds are selected by picking, but I can’t rotate any group from either side 
>> of the bond. Am I missing something (key modifier for example ?)
>> Thanks for your help,
>> Paul
>> --
>> ___
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> 
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[Jmol-users] set picking rotate bond broken ?

2015-11-11 Thread Paul PILLOT

Hi,
I am wondering if the « set picking rotatebond » command is broken ? I’ve tried 
bot with the application (v 14.5.0_2015.11.06) and the HTML5 jsmol flavour
Bonds are selected by picking, but I can’t rotate any group from either side of 
the bond. Am I missing something (key modifier for example ?)
Thanks for your help,
Paul
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Re: [Jmol-users] Request for help: Outlines for atoms (and bonds)

2015-11-10 Thread Paul PILLOT

halos mays  also be an option
http://chemapps.stolaf.edu/jmol/docs/#halos

-Paul
> Le 10-11-2015 à 14:35, Angel Herráez  a écrit :
> 
> Oh yes!
> 
> Go to the documentation page,
> http://chemapps.stolaf.edu/jmol/docs/
> and search for "outline"
> and you have
> set celShading TRUE
> set celShadingPower (integer)
> 
> Is that what you were looking for? So it seems to me
> 
> 
> 
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Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

2015-11-03 Thread Paul PILLOT

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  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!
> 
> 
> 
> 
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Re: [Jmol-users] Showing CIF atoms at vertices of the cell

2015-10-15 Thread Paul PILLOT

try « packed » 

Paul

> Le 15-10-2015 à 14:30, Xavier Prat-Resina  a écrit :
> 
> Hello,
> 
> I'm trying to display the unit cell of ZnS from a CIF file by using:
> 
> load ZnS_blende.cif {1 1 1}
> 
> See here: http://chemdata.r.umn.edu/jmol/blende.html 
> 
> 
> However, as you can see jmol does not show all the zinc atoms at the vertices 
> of the cell.
> 
> The atoms at (x=1,y=1 or z=1) are there when I load a {2 2 2} cell.
> 
> Is there any keyword that allows me to show all atoms when loading {1 1 1}?
> 
> Thanks
> 
> Xavier
> 
> 
> --
> Xavier Prat-Resina
> Assistant Professor, Chemistry.
> University of Minnesota Rochester.
> 111 South Broadway, Suite 300
> Rochester, Minnesota 55904
> 
> Phone: 507-258-8215
> E-mail: pratr...@r.umn.edu 
> https://sites.google.com/a/r.umn.edu/prat-resina/ 
> 
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Re: [Jmol-users] JSmol/HTML5 - Forced usage

2015-10-01 Thread Paul PILLOT

Hi Rolf,
the only way to override the info setting I know about is through the URL, by 
adding a flag :
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Setting_parameters_from_the_URL

-Paul

> Le 01-10-2015 à 10:37, Rolf Huehne  a écrit :
> 
> Hi all,
> 
> is there a way to force JSmol to use HTML5 and not Java instead of just 
> providing a priority list?
> 
> My problem is that JSmol 14.3.16_2015.09.28 on a specific page always 
> runs the Java version even though the priority is set to "HTML5" and 
> "JAVA" isn't even included in the priority list. This prevents to do any 
> debugging to find out what might be wrong.
> 
> The switch between Java and HTML5 works with the same version in the 
> 'Jena3D Viewer'. The page where it doesn't work is actually a static 
> copy of a 'Jena3D Viewer' page, so except for some adapted URLs the 
> pages are identical and both should work with HTML5.
> 
> Regards,
> Rolf
> 
> -- 

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Re: [Jmol-users] PubChem Widget

2015-09-19 Thread Paul PILLOT

Hi Otis,
this is a very impressive website, thank-you for the link.

I’ve found the documentation for the Pubchem autocomplete widget : 
https://pubchem.ncbi.nlm.nih.gov/widget/docs/widget_autocomplete_help.html 

-Paul

> Le 19-09-2015 à 09:32, Otis Rothenberger  a écrit :
> 
> Maybe this is well known, but I just learned about it from a college freshman 
> in the Netherlands. PubChem has an auto-complete widget that is pretty 
> incredible. If you have not seen this in action, take a look at his site, 
> MolView:
> 
> http://molview.org 
> 
> Click Continue on the splash screen and look for the search box in the upper 
> left hand corner. Type something, it speaks for itself. Obviously multiple 
> dictionaries are being used. He told me something about this a while back, 
> but it went right over my head. I never checked it out until yesterday, 
> perhaps because auto complete usually gets on my nerves. This is definitely 
> an exception.
> 
> I know what I working on this week end! 
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.com 
> http://chemagic.com
> 
> --
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Re: [Jmol-users] try again

2015-09-16 Thread Paul PILLOT

You’re right : jsmol.htm indeed works like a charm !
Paul

> Le 16-09-2015 à 09:16, J. Bays  a écrit :
> 
> Paul: I think that is intentional. Try jsmol.htm.  It is the same test without
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's Collegethe images. 
> Norte Dame, IN
> 
> Sent from my iPad
> 


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Re: [Jmol-users] try again

2015-09-16 Thread Paul PILLOT

Everything works as expected (including localization alerts, filter2D, 
fractional coordinates shorthand notation) ! Thanks a lot Bob !

The only remaining glitch is in the test2.htm page that displays 2 still images 
in the forefront, having the active molecule displayed ind the background.
It appears on the two browsers I’ve checked. It doesn’t appear in any of the 
other pages I’ve tried so it should only be related to a code in this specific 
page.

Here are the images :
- screen shot of the jsmol window : screen_capture.png 

- image of the windows as computed per jsmol (image command) : test2_jsmol.png 

-Paul

> Le 16-09-2015 à 03:49, Angel Herráez  a écrit :
> 
> simple.htm  runs ok now here, without errors and the language is correct (it 
> also was before)
> 
> On 16 Sep 2015 at 0:00, Robert Hanson wrote:
>> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_
>> 2015.09.15-binary.zip
>> 
>> Jmol.___JmolVersion="14.3.16_2015.09.15"
> 

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Re: [Jmol-users] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Paul PILLOT

The language bug is still present (to test this, set up your browser language 
to another than english).
-Paul

> Le 14-09-2015 à 19:15, Robert Hanson  a écrit :
> 
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.09.14-binary.zip
>  
> 
> 
> Jmol.___JmolVersion="14.3.16_2015.09.14"
> 
> bug fix: load data [2D mol structure...] filter "2D" not working
> bug fix: Crystallographic Open Database CIF files have unusual 
> atom_site_label ("MgT") 
>  and no atom_site_type_symbol, leading to missing element assignments
> 
> 
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Paul PILLOT

Here is the test :
- I’ve downloaded jsmol (extracted from jmol-14.3.16_2015.09.14.zip) and copied 
the folder in a repository on my local Apache web server
- from the browser (same results with Firefox, Safari and Chrome on Mac OS X 
10.10.5), I run the test2.htm page
- I get the 4 following alert messages :

1st :
"[Java2Script] The required class file 

j2s/J/translation/Jmol/fr/Messages_fr.js
could not be loaded. Script error: expected expression, got '<' 

data:



404 Not Found

Not Found
The requested URL /jmol/jsmol/j2s/J/translation/Jmol/fr/Messages_fr.js was 
not found on this server.

Apache Server at chemapps.stolaf.edu Port 80




0 function (file, file0, js) 
1 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
2 function (name, onLoaded, forced, async, mode) 
3 function (clazzName, applet, state) 
4 J.api.Interface.getInterface(name, vwr, state) 
5 J.i18n.Resource.getResource(vwr, className, name) 
6 J.i18n.GT.addBundle(vwr, className, name) 
7 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
8 construct(vwr, langCode) 
9 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
10 function (id, objThis, claxxRef, fxName, args, _saem) 
11 function () 
12 function (objThis, args) 
13 function () 
14 J.i18n.GT.getTextWrapper() 
15 J.i18n.GT._(string) 
16 function () 
17 function (node, _updateNode) 
 »

2nd message :
"SyntaxError: Unexpected token '<' loading file 
j2s/J/translation/Jmol/fr/Messages_fr.js J.translation.Jmol.fr.Messages_fr 
0 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
1 function (name, onLoaded, forced, async, mode) 
2 function (clazzName, applet, state) 
3 J.api.Interface.getInterface(name, vwr, state) 
4 J.i18n.Resource.getResource(vwr, className, name) 
5 J.i18n.GT.addBundle(vwr, className, name) 
6 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
7 construct(vwr, langCode) 
8 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
9 function (id, objThis, claxxRef, fxName, args, _saem) 
10 function () 
11 function (objThis, args) 
12 function () 
13 J.i18n.GT.getTextWrapper() 
14 J.i18n.GT._(string) 
15 function () 
16 function (node, _updateNode) 
 »

3rd message :
"[Java2Script] The required class file 

j2s/J/translation/JmolApplet/fr/Messages_fr.js
could not be loaded. Script error: Unexpected token '<' 

data:



404 Not Found

Not Found
The requested URL 
/jsmol/jmol-14.3.16_2015.09.14/jsmol/j2s/J/translation/JmolApplet/fr/Messages_fr.js
 was not found on this server.




0 function (file, file0, js) 
1 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
2 function (name, onLoaded, forced, async, mode) 
3 function (clazzName, applet, state) 
4 J.api.Interface.getInterface(name, vwr, state) 
5 J.i18n.Resource.getResource(vwr, className, name) 
6 J.i18n.GT.addBundle(vwr, className, name) 
7 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
8 construct(vwr, langCode) 
9 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
10 function (id, objThis, claxxRef, fxName, args, _saem) 
11 function () 
12 function (objThis, args) 
13 function () 
14 J.i18n.GT.getTextWrapper() 
15 J.i18n.GT._(string) 
16 function () 
17 function (node, _updateNode) 
 »

4th message :
"SyntaxError: Unexpected token '<' loading file 
j2s/J/translation/JmolApplet/fr/Messages_fr.js 
J.translation.JmolApplet.fr.Messages_fr 
0 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
1 function (name, onLoaded, forced, async, mode) 
2 function (clazzName, applet, state) 
3 J.api.Interface.getInterface(name, vwr, state) 
4 J.i18n.Resource.getResource(vwr, className, name) 
5 J.i18n.GT.addBundle(vwr, className, name) 
6 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
7 construct(vwr, langCode) 
8 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
9 function (id, objThis, claxxRef, fxName, args, _saem) 
10 function () 
11 function (objThis, args) 
12 function () 
13 J.i18n.GT.getTextWrapper() 
14 J.i18n.GT._(string) 
15 function () 
16 function (node, _updateNode) 

« 

The interactive menu appears in french and I am finding striking that there is 
no j2s/J/translation folder at all (even if the script apparently search for a 
js file in that folder) ?!

If I switch the browser language preference to english first, I don’t get any 
error message.
If I switch it to spanish ([es]), I get the 4 alert messages (see infra). Same 
for German ([de]) (see infra).

1st message for spanish
"Java2Script] The required class file 

j2s/J/translation/Jmol/es/Messages_es.js
could not be loaded. Script error: expected expression, got '<' 

data:



404 Not Found

Not Found
The requested URL 
/jsmol/jmol-14.3.16_2015.09.14/jsmol/j2s/J/translation/Jmol/es/Messages_es.js 
was not found on this server.




0 function (file, file0, js) 
1 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
2 function (name, onLoaded, forced, async, mode) 
3 function (clazzName, applet, state) 
4

Re: [Jmol-users] Jmol -- testing requested -- load filter "2D" not working

2015-09-14 Thread Paul PILLOT

Well, it did work… 3 years ago…
I’ve implemented this in a previous page that I haven’t touched for a while. 
The migration to HTML5 is now overdue and I wanted to update to the latest 
version (and take profit of the speed bump in JS execution). 
The workaround you are suggesting indeed works, but the original filter "2D", 
was quicker at rendering the model. Maybe a reduced number of minimization 
steps was involved ? Or just the fact that the pre minimization state was not 
displayed and only the resulting computed model ?
Paul

> Le 14-09-2015 à 00:58, Otis Rothenberger <osrot...@chemagic.com> a écrit :
> 
> Hi Paul,
> 
> I played with this for a while. Did Filter “2d” ever work with load data? I 
> keep getting jmol script errors if I try to incorporate the filter. I tried 
> several locations for insertion.
> 
> This alternative gets the job done:
> 
> load DATA "model"
> Ethane
> 
> http://www.ichemlabs.com <http://www.ichemlabs.com/>
>   2  1  0  0  0  0999 v2000
>-0.4330   -0.25000. C   0  0  0  0  0  0
> 0.43300.25000. C   0  0  0  0  0  0
>   1  2  1  0 0  0
> M  END "model";calculate hydrogens;minimize
> 
> Otis
> 
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com <mailto:o...@chemagic.com>
> http://chemagic.com
> 
>> On Sep 13, 2015, at 11:26 PM, Paul PILLOT <paulpil...@gmail.com 
>> <mailto:paulpil...@gmail.com>> wrote:
>> 
>> Hi Jmolers,
>> I’ve tried with the 2 latest versions of Jmol (14.3.16, 14.2.15) and they 
>> both seem broken in respect with this command.
>> 
>> Test case :
>> copy and paste the following in Jmol console :
>> 
>> load DATA "model"
>> Ethane
>> 
>> http://www.ichemlabs.com <http://www.ichemlabs.com/>
>>   2  1  0  0  0  0999 v2000
>>-0.4330   -0.25000. C   0  0  0  0  0  0
>> 0.43300.25000. C   0  0  0  0  0  0
>>   1  2  1  0 0  0
>> M  END "model" filter "2D"
>> 
>> 
>> It displays only 2 atoms of carbon instead of adding the required hydrogen 
>> and minimizing.
>> 
>> -Paul
>> --
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[Jmol-users] Jmol -- testing requested -- load filter "2D" not working

2015-09-13 Thread Paul PILLOT

Hi Jmolers,
I’ve tried with the 2 latest versions of Jmol (14.3.16, 14.2.15) and they both 
seem broken in respect with this command.

Test case :
copy and paste the following in Jmol console :

load DATA "model"
Ethane

http://www.ichemlabs.com
  2  1  0  0  0  0999 v2000
   -0.4330   -0.25000. C   0  0  0  0  0  0
0.43300.25000. C   0  0  0  0  0  0
  1  2  1  0 0  0
M  END "model" filter "2D"


It displays only 2 atoms of carbon instead of adding the required hydrogen and 
minimizing.

-Paul--
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Re: [Jmol-users] get {} value without knowing key?

2015-08-30 Thread Paul PILLOT

print x[x.keys[3]] works, but there might exist a shorter way of doing this…

-Paul

 Le 30-08-2015 à 20:49, Eric Martz ema...@microbio.umass.edu a écrit :
 
 load =1al4
 x = {altloc!=}.altloc.all.pivot
 
 Now we have an associative array with key:value pairs:
 
 $ print x
 {
   A  :  238
   B  :  244
   C  :  34
   D  :  12
  }
 $ print x.type
 hash
 
 I can retrieve the value for key C:
 
 $ print x..C
 34
 
 How do I retrieve a value for the nth element of the array without knowing 
 the key?
 
 $ print x.keys[3]
 C
 
 $ print x..x.keys[3]
 (prints blank)
 
 Thanks, Eric
 
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Re: [Jmol-users] Jmol -- testing requested

2015-08-25 Thread Paul PILLOT

Hi Bob,
the 2 error messages on startup are displayed on MacOS X.10.5, Safari 8.0.8

TypeError: undefined is not an object (evaluating 
'J.api.Interface.getInterface') try/catch path:
0 function (b, d) 
 args[0]=TypeError: undefined is not an object (evaluating 'J.api.Int...
 args[1]=function () {a.instantialize(this,arguments);}
1 J.i18n.GT.addBundles(a, c, d, b, f) 
 args[0]=null
 args[1]=J.translation.Jmol.
 args[2]=null
 args[3]=null
 args[4]=fr
2 construct(a, c) 
 args[0]=null
 args[1]=null
3 function () 
 args[0]=null
 args[1]=null
4 function (a, b) 
 args[0]=[J.i18n.GT object]
 args[1]=,
5 function () 
 args[0]=null
 args[1]=null
6 J.i18n.GT.getTextWrapper() 
7 J.i18n.GT._(a) 
 args[0]=assign/new atom or bond (requires {0})
8 function () 
9 function (a) 
recursing

and 

TypeError: undefined is not an object (evaluating 
'J.api.Interface.getInterface') try/catch path:
0 function (b, d) 
 args[0]=TypeError: undefined is not an object (evaluating 'J.api.Int...
 args[1]=function () {a.instantialize(this,arguments);}
1 J.i18n.GT.addBundles(a, c, d, b, f) 
 args[0]=null
 args[1]=J.translation.JmolApplet.
 args[2]=null
 args[3]=null
 args[4]=fr
2 construct(a, c) 
 args[0]=null
 args[1]=null
3 function () 
 args[0]=null
 args[1]=null
4 function (a, b) 
 args[0]=[J.i18n.GT object]
 args[1]=,
5 function () 
 args[0]=null
 args[1]=null
6 J.i18n.GT.getTextWrapper() 
7 J.i18n.GT._(a) 
 args[0]=assign/new atom or bond (requires {0})
8 function () 
9 function (a) 
recursing

I also get an error message when trying to display the contextual menu with 
jsmol.
TypeError: undefined is not a function (evaluating 'a.getHtml5Applet()') 
try/catch path:
0 function (b, d) 
 args[0]=TypeError: undefined is not a function (evaluating 'a.getHtm...
 args[1]=function () {a.instantialize(this,arguments);}
1 J.awtjs2d.Platform.getMenuPopup(a, c) 
 args[0]=null
 args[1]=j
2 JV.Viewer.getPopupMenu() 
3 JV.Viewer.popupMenu(a, b, d) 
 args[0]=676
 args[1]=188
 args[2]=j
4 JV.ActionManager.checkPressedAction(a, c, b) 
 args[0]=676
 args[1]=188
 args[2]=false
5 JV.ActionManager.mouseAction(a, c, b, e, f, g) 
 args[0]=4
 args[1]=1440526426898
 args[2]=676
 args[3]=188
 args[4]=0
 args[5]=4
6 J.awtjs2d.Mouse.pressed(a, c, d, b) 
 args[0]=1440526426898
 args[1]=676
 args[2]=188
 args[3]=4
 args[4]=false
7 J.awtjs2d.Mouse.processEvent(a, c, d, b, f) 
 args[0]=501
 args[1]=676
 args[2]=188
 args[3]=4
 args[4]=1440526426898
8 JV.Viewer.processMouseEvent(a, c, b, e, f) 
 args[0]=501
 args[1]=676
 args[2]=188
 args[3]=4
 args[4]=1440526426898
9 J.appletjs.Jmol.processMouseEvent(a, c, d, b, f) 
 args[0]=501
 args[1]=676
 args[2]=188
 args[3]=4
 args[4]=1440526426898

Paul

 Le 25-08-2015 à 11:58, Rolf Huehne rhue...@fli-leibniz.de a écrit :
 
 On 08/25/2015 04:28 PM, Robert Hanson wrote:
 OK, let's try again, please. I really appreciate all this testing. Rolf, I
 am especially interested in if this fixes your JenaLib startup problem.
 
 http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.25-binary.zip/download
 
 Thanks, Bob. On Linux the startup problem is gone now and the console 
 opens up in JSmol. I will try later at home on MacOS.
 
 Regards,
 Rolf
 -- 
 
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 Postdoc
 
 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
 Beutenbergstrasse 11
 07745 Jena, Germany
 
 Phone:   +49 3641 65 6205
 Fax: +49 3641 65 6210
 E-Mail:  rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.de
 
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Head of Administration: Dr. Daniele Barthel
 Chairman of Board of Trustees: Dennys Klein
 
 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
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Re: [Jmol-users] Jmol -- testing requested

2015-08-25 Thread Paul PILLOT

Thanks Otis,
I am also running pages from my local web server (localhost). I haven’t spotted 
the setting you are referring to. 
I have made further tests with firefox 40 and Chrome 44.
The three browsers give the same consistent error messages (that don’t prevent 
jsmol from working).

Paul

 Le 25-08-2015 à 14:34, Otis Rothenberger osrot...@chemagic.com a écrit :
 
 Bob and Paul,
 
 I’m not seeing this (below) in MacOS X 10.10.4 (Yosemite) and Safari 8.0.7.
 
 I should mention that I’m running locally with internet connection - i.e. all 
 my AJAX remote calls working.
 
 This means that I run Safari with “Disable Local File Restrictions” checked.
 
 Otis
 
 --
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 o...@chemagic.com
 http://chemagic.com
 


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Re: [Jmol-users] Jmol speed

2014-03-02 Thread Paul Pillot

Maybe because you’re mentioning it, it indeed looks faster. 
I’ve also tried the webGL demo and I am sorry to report that it’s broken 
http://chemapps.stolaf.edu/jmol/jsmol/jsmolgl.htm
Paul

Le 2 mars 2014 à 00:02, Robert Hanson hans...@stolaf.edu a écrit :

 Is it just my wishful thinking, or does it seem like this version of Jmol at 
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm is faster and smoother than 
 previous versions? 
 
 Thanks to Otis and Ron and Angel and Charles and Alexander for the timely 
 observations this week.
 
 I plan to release Jmol 14.0.11 and 14.1.11 (identical) next Tues or Wed. 
 Please test! Latest is at http://chemapps.stolaf.edu/jmol/zip/Jmol.zip just 
 uploaded today.
 
 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] Question: What is the preferred way to save JSmol state and orientation?

2014-01-31 Thread Paul Pillot

Hi Chuck,
have you tried « get property stateInfo » ? It should restore everything 
including orientation, zoom, etc…
Paul

Le 31 janv. 2014 à 16:32, Charles Harrison Shubert cshub...@mit.edu a écrit :

 Hi,
 
 When my users open my app, I'd like for JSmol to be in the same state that 
 they left it in. My users can generate quite a bit of JSmol script. 
 Currently, I'm using the browser's localStorage to store app state in a JSON 
 object.
 
 What would be the preferred way to extract JSmol state including rendering, 
 orientation, zoom, etc, to save for my user's next visit?  I can imagine 
 accumulating the user's JSmol script, saving it, and using it to restore 
 JSmol, but I'm not sure how to save the orientation.
 
 I'd appreciate any thoughts that you have on this.
 
 Thanks,
 
 --Chuck
 
 
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[Jmol-users] JSmol HTML5 code : remaining /div

2013-12-11 Thread Paul Pillot

Hi,
trying to debug one of my webpages that doesn’t display the HTML5 Jmol (without 
throwing any error) but that does display the Java version, I’ve looked at the 
generated code (jmolApplet0._code) and saw this for the canvas2D version :

/divdiv id=jmolApplet0_2dappletdiv 
style=position:absolute;width:100%;height:100%;overflow:hidden;display:none/divdiv
 id=jmolApplet0_infotablediv 
style=width:100%;height:100%;position:absolute;top:0px;left:0pxdiv 
id=jmolApplet0_infoheaderdiv 
style=height:20px;width:100%;background:yellow;display:nonespan 
id=jmolApplet0_infoheaderspan/spanspan id=jmolApplet0_infocheckboxspan 
style=position:absolute;text-align:right;right:1px;a 
href=javascript:Jmol.showInfo(jmolApplet0,false)[x]/a/span/divdiv 
id=jmolApplet0_infodiv 
style=position:absolute;top:20px;bottom:0px;width:100%;height:100%;overflow:auto/div/div/divbr
 /input type=text id=jmolApplet0_query 
onkeypress=if(13==event.which){Jmol._applets['jmolApplet0']._search();return 
false} size=32 value= /br /nobrselect 
id=jmolApplet0_selectoption value=$ selectedNCI(small 
molecules)/optionoption value=: PubChem(small molecules)/optionoption 
value== RCSB(macromolecules)/option/selectbutton 
id=jmolApplet0_submit 
onclick=Jmol._applets['jmolApplet0']._search()Search/button/nobr »

I think that the first closing div might break my design, preventing the 
display.

The java version HTML code generated doesn’t begin by a closing tag.

-Paul


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Re: [Jmol-users] Safari test -- fixes Boolean issue?

2013-12-03 Thread Paul Pillot

It works !
Mac OSX.9 Safari Version 7.0 (9537.71)
(the display is a lot slower than what I get with firefox)

Paul

Le 3 déc. 2013 à 13:54, Robert Hanson hans...@stolaf.edu a écrit :

 and http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 and http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm
 
 
 On Tue, Dec 3, 2013 at 12:11 PM, Robert Hanson hans...@stolaf.edu wrote:
 http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.03a.zip
 
 -- 
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 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
 
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Re: [Jmol-users] local testing ready iteration 1,203,304,440

2013-11-29 Thread Paul Pillot

If you have access to your server’s feature, you can also enable gzip 
compression (on Apache it’s the mo_deflate program) for the associated plain 
text format. Then the server and the browser will do the job !
Paul
Le 28 nov. 2013 à 13:12, Rolf Huehne rhue...@fli-leibniz.de a écrit :

 On 11/28/2013 06:15 PM, Robert Hanson wrote:
 The files are loading, so Jmol is recognizing them as binary. I'll add
 
 Jmol._alertNoBinary
 
 that you can set false.
 
 But, really, you're doing a double send -- once to the relay host in
 binary, then again in BASE64 to JSmol, then a decoding back into binary. So
 think about if there is a way to avoid that. They are just PDB or mmCIF
 files, right?
 
 Yes, for usage with Jmol they are currently gzip-compressed PDB files.
 
 If someone could tell me a way to convince browsers to uncompress 
 gzip-compressed CGI output before feeding it into JSmol I would be happy 
 to implement it.
 
 Sending them uncompressed instead is not really an option. Especially 
 the biological unit files can get very large, even compressed.
 Before I figured out how to activate the binary file loading in JSmol it 
 was done this way. But it took very long to load a file with a 
 compressed size of ~2 megabyte on a 2 MBit/s connection. Even with the 
 double send it was several times faster with activated binary file 
 loading of the compressed file.
 
 Regards,
 Rolf
 -- 
 
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 Postdoc
 
 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
 Beutenbergstrasse 11
 07745 Jena, Germany
 
 Phone:   +49 3641 65 6205
 Fax: +49 3641 65 6210
 E-Mail:  rhue...@fli-leibniz.de
 Website: http://www.fli-leibniz.de
 
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Head of Administration: Dr. Daniele Barthel
 Chairman of Board of Trustees: Dennys Klein
 
 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228
 
 
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Re: [Jmol-users] How to set up a molecular playground

2013-09-21 Thread Paul Pillot

Dear Angel,
thank-you for your answer.
I've sent a message to Craig Martin, but he might be busy at the moment. I am 
also wondering at the scripts and the way
they succeed from one to another. Bob mentions in the source code that he uses 
a simple Excel spreadsheet
with 3 columns. I have found it there : 
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/molecularplayground/
under biophysics.xlsx

Another related question : have you chosen to translate the material from 
proteopedia in spanish ?

Paul
 
Le 21 sept. 2013 à 06:22, Angel Herráez a écrit :

 Dear Paul,
 
 Good you want to increase the collection of MP installations!
 
 I got the sofware from the developers at UMass, specifically Craig Martin. 
 Then in order to use some recent Jmol features, I needed an update in the 
 software that was also made and provided by them.
 On the other hand, Bob Hanson is running a slightly different version on his 
 site (I need some time to dig out the details on that, it's mostly the way to 
 store and deliver the scripts).
 
 I'm afraid that the code is not completely integrated into Jmol's source.
 
 I wil be happy to share my software setup with you if you wish.
 
 
  I have also found some references on the dev list to the moleK project that 
  does not use
  MPKinectDriver and seems to run on linux systems
 
 I don't know about that one. The existing MolecularPlayground software runs 
 only in a Mac since the interface with the Kinect was programmed for MacOS.
 
 Let's keep talking about this.
   

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[Jmol-users] How to set up a molecular playground

2013-09-20 Thread Paul Pillot

Dear Jmolers,
I would like to set up a Molecular playground. I have read extensively the 
molecularplayground.org website, but I could not find any information regarding 
the software used nor download it.
After some googling, I've seen on Angel's dedicated webpage that MPControlHub 
and MPJmolApp are required.
I have found MPJmolApp in Jmol's source code.
I have also found some references on the dev list to the moleK project that 
does not use MPKinectDriver and seems to run on linux systems

So, where should I start ? Can someone explain how the software part of the 
setup can be done ? Plus, is a mac required to run it ?

Thank you for your help,
Paul

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Re: [Jmol-users] Some Desirable Features!

2013-09-12 Thread Paul Pillot

I think it is possible through the javascript file api to get access to the 
content of a local file, 
and then send this content to Jsmol with the load data function.
The drawback is that the file api is not well supported across all browsers, at 
least I've tried it
successfully with firefox a couple of years ago.
For file export, the file api has some capabilities but it is even more 
scarcely supported 
Paul

Le 12 sept. 2013 à 10:40, Amjad Farooq a écrit :

 Angel,
 
 Thanks for your advice. 
 
 But, I think I would continue using Jmol for now but switch to JSmol when  
 the file upload/save feature becomes available. That is very important to me 
 and I cannot do away with it.
 
 Nonetheless, kudos to you and all other JSmol developers for improving its 
 speed and many other features. Great stuff.  
 
 Keep up the good work.
 Amjad
 
 
 
 
 On Thu, Sep 12, 2013 at 3:18 AM, Angel Herráez angel.herr...@uah.es wrote:
 Hi Amjad
 
  (2) Is it possible to provide a more user-friendly javascript syntax for
  JSmol that directly builds upon the Jmol syntax (which most of us are
  familiar with and thus would make it easier to switch between the two
  easily)?
 
 Have you looked at the Jmol2.js library? It allows you to keep the classical
 syntax and internally converts it to the new one.
 http://wiki.jmol.org/index.php/JSmol#Conversion_using_the_Jmol2.js_.27ada
 pter.27_library
 
 I personally think it is better to move into applying the new syntax, though.
 
 There is also a bigger issue if you make a page that holds more than one
 Jmol Object. Then you must be more careful with the syntax and there are
 some differences in the way they are addressed now, but the object-oriented
 method of JSmol should be more easily managed in this cases.
 
 Finally don't forget that the new (JSmol) Jmol-JSO constructs also allow to
 use the Jmol Java applet.
 
 
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Re: [Jmol-users] JSmol too slow!

2013-09-10 Thread Paul Pillot

Try: 

Jmol.script(jmolAppletObjectNameComesHere,load =PDBID)

where jmolAppletObjectNameComesHere is the name you gave to your jmol object 
instance at creation

Paul

Le 10 sept. 2013 à 18:01, Amjad Farooq a écrit :

 Bob,
 
 I checked out your new JSmol page with the protein loaded in at:
 http://chemapps.stolaf.edu/jmol/jsmol/simple.htm
 
 The response time for this JSmol page is very fast and on par with Jmol. I 
 see no differences between the two with this new JSmol javascript that you 
 are using. So, kudos to you! And this is really cool development. Heck with 
 this Java nonsense. I am gonna switch to JSmol and use it exclusively from 
 now on. It is much easier and more widely acceptable as many of my 
 collaborators do not have Java installed on their machines. Thank you!
 
 One quick question:
 I notice that you also incorporated JmolButton, JmolCheckbox and JmolMenu 
 into JSmol. But, how do I use JmolScript feature of Jmol in JSmol?! For 
 example, I use the following javascript a lot in my Jmol:
 
 script type=text/javascript 
 function pdb() { 
 jmolScript(load =PDBID)
 /script
 button onClick=pdb();Load PDB/button
 
 How do I use the JmolScript syntax in JSmol?
 
 Thanks,
 Amjad
 
 
 
 
 
 
 
 
 On Tue, Sep 10, 2013 at 3:18 PM, Robert Hanson hans...@stolaf.edu wrote:
 Angel, I'd appreciate your assessment of 
 
 set platformSpeed
 
 Are there settings that you prefer for specific types of compounds? What 
 would you recommend for proteins in general? 
 
 Bob
 
 
 
 On Mon, Sep 9, 2013 at 12:51 PM, Angel Herráez angel.herr...@uah.es wrote:
  Something odd there. That's not been our experience.
 
 Well, my experience is that Java Jmol is faster than JSmol. Of course
 this has improved a lot in the las few months and now it's rather
 tolerable, and all depends on the size of the molecule loaded and
 even personal perception, but for me yes, Java is still more agile in
 both loading and responsiveness of the model.
 
 I am not denying the need to move forward into non-Java systems and
 the excellent achievement in JSmol and prospects for the future.
 
 
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Re: [Jmol-users] jsmol issue

2013-09-08 Thread Paul Pillot

Not exactly the subject, but when downloading a pdb file from RCSB website, the 
server checks if the browser accepts compressions and compress the pdb file on 
the file. You don't have to explicitly request a pdb.gz file to get the 
benefits from data compression.
Paul

Le 8 sept. 2013 à 08:25, Geoffrey Rowland a écrit :

 I *think* I understand what is going on here.
 
 The problem appears due to inconsistencies in the way the pdb files are 
 gzipped up
 
 In my jsmol /data folder:
 
 1crn.pdb.gz is not actually gzipped at all, just a plain text file identical 
 to 1crn.pdb. However, if 1crn.pdb is gzipped to make a bona fide 1crn.pdb.gz, 
 it still works!
 
 1m19.pdb.gz contains 1M19.pdb. Note the uppercase M. If a consistently 
 lowercase gzip bundle is made, it works!
 
 3hz7.pdb.gz contains 3hz7x.pdb. Note the extra x!. If the x is removed and 
 the gzipped archive reconstructed, everything works!
 
 My local webserver, and most of my testing, has been on Fedora Linux. So, may 
 have displayed case-sensitivity issues not occurring on Windows.
 
 Hope that helps someone.
 
 
 
 On 8 September 2013 12:26, Geoffrey Rowland rowland.ge...@gmail.com wrote:
 Err... Actually though .pse files now work with Chrome, I am still seeing an 
 issue with some .pdb.gz files  (e.g. data/1m19.pdb.gz, data/3hz7.pdb.gz) 
 though data/1crn.pdb.gz still works!
 
 Forgot the RCSB links were now using .pdb rather than .pdb.gz and can't 
 easily check against the Stolaf server as jsmol.htm does not have any .pdb.gz 
 links.
 
 Anyway, not a 'show stopper' as can use the .pdb files instead.
 
 Cheers
 
 
 
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Re: [Jmol-users] language localization for JSmol

2013-03-21 Thread Paul Pillot

It works great now !
Bravo !
Paul

Le 22 mars 2013 à 03:08, Robert Hanson a écrit :

 OK, the Chrome business should be fixed.  
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 
 
 
 
 
 On Thu, Mar 21, 2013 at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote:
 OK, the problem with Chrome is that we need the server relay for loading 
 binary files, and the PO files are binary files, or at least that's how I'm 
 reading them. (Unless someone knows a way to have AJAX read UTF-8 files in 
 regular string mode. That would be very helpful.) If not, then that will 
 never work for local pages, and hosted pages will need a relay that can 
 convert those to do that. 
 
 Bob
 
 
 On Thu, Mar 21, 2013 at 5:28 AM, Angel Herráez angel.herr...@uah.es wrote:
 More testing:
 
 Firefox:
  - all OK
 
 Chrome:
  - console and menu display in English
  - J.i18n.GT.getLanguage()  reports  es
  - popup menu reports Spanish option selected
  - switching languages via menu does not work
 
 Opera
  - all OK:
  - console and menu display in Spanish
  - switching languages via menu OK
 
 IE8
  - cannot test now due to the error in loading JSmol
 
 
 
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 St. Olaf College
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 http://www.stolaf.edu/people/hansonr
 
 
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Re: [Jmol-users] About adjustment of jmol applet window size by mouse

2013-03-20 Thread Paul Pillot

plus 

set antialiasdisplay true

-Paul

Le 20 mars 2013 à 19:46, Angel Herráez a écrit :

 But the cartoons structure of my test applet looks not very smooth and has 
 jagged edges.
 I am wondering if there are any other features to get smoother structure.
 
 It may depend on your particular molecule, but yes you can control 
 smoothing of the cartoons. See the documentation:
 http://chemapps.stolaf.edu/jmol/docs/#cartoon
 
 set hermiteLevel
 set ribbonAspectRatio 
 
 
 
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Re: [Jmol-users] language localization for JSmol

2013-03-20 Thread Paul Pillot

The message is still in english for me
Tested on OSX.6 Chrome Version 25.0.1364.172 in french after clearing the cache.
-Paul

Le 20 mars 2013 à 20:54, Robert Hanson a écrit :

 I've updated that after Angel's helpful tests. It should be working now:
 
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 
 If your browser's default language is not English, could you please go to 
 that page and click on console just below the applet and see if the message 
 is in English or your language? 
 
 Provided this works, it means that all the language translation in Jmol is 
 automatically ported to JSmol.
 
 
 Thanks,
 
 Bob
 
 

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Re: [Jmol-users] language localization for JSmol

2013-03-20 Thread Paul Pillot

After further testing,
firefox displays JSmol in french as expected.
chrome doesn't (still in english), the version number is the exact same as the 
one you described (apparently there is no cache concern involved)

What is the language flag checked for enabling localization ?

Paul

Le 21 mars 2013 à 01:14, Robert Hanson a écrit :

 Paul, what does that console show (please click the show info link and find 
 the information about the language, as Angel has shown). Could still be a 
 version issue. It should read 
 
 Jmol Version: 13.1.14_dev19 $Date: 2013-03-20 22:42:37 -0500 (Tue, 19 Mar 
 2013) $
 
 You could also enter this in the developer console:
 
 J.i18n.GT.getLanguage()
 
 or
 
 Jmol.featureDetection.getDefaultLanguage()
 
 
 
 Bob
 
 
 
 On Wed, Mar 20, 2013 at 3:07 PM, Paul Pillot 
 paul.pil...@ac-orleans-tours.fr wrote:
 The message is still in english for me
 Tested on OSX.6 Chrome Version 25.0.1364.172 in french after clearing the 
 cache.
 -Paul
 
 Le 20 mars 2013 à 20:54, Robert Hanson a écrit :
 
 I've updated that after Angel's helpful tests. It should be working now:
 
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 
 If your browser's default language is not English, could you please go to 
 that page and click on console just below the applet and see if the 
 message is in English or your language? 
 
 Provided this works, it means that all the language translation in Jmol is 
 automatically ported to JSmol.
 
 
 Thanks,
 
 Bob
 
 
 
 
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[Jmol-users] WebGL version broken ?

2013-03-11 Thread Paul Pillot

Apparently the WebGL version is broken on test2.htm
Chrome's console says :
Uncaught TypeError: Cannot read property '_is2D' of undefined (JSmol.js:206)
Paul

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Re: [Jmol-users] issues with converting to jsmol

2013-02-24 Thread Paul Pillot

works for me on OsX with Chrome :
inline: Capture d’écran 2013-02-20 à 22.42.32.png
-Paul

Le 20 févr. 2013 à 22:24, Jennifer L. Muzyka a écrit :

 I'm working on converting pages from Jmol to JSmol and am seeing a strange 
 and mysterious phenomenon, with the structures showing up in a different part 
 of the page than what I expect based on the coding.  I'm using Bootstrap to 
 handle the layout, in case that's relevant.
 
 Here's the Jmol version of the page, so you can see the layout I'm aiming 
 for:  http://web.centre.edu/muzyka/organic/jmol/tutorials/butanes.htm.  The 
 JSmol version of the page is 
 http://web.centre.edu/muzyka/organic/jsmol/butanes.htm.  
 
 I would appreciate any insights anybody can offer about why the structures 
 don't show up in the places where I expected them.  Thanks.
 Jennifer
 
 
 
 
 
 
 
 Jennifer L. Muzyka
 Professor of Chemistry
 Centre College
 600 West Walnut Street
 Danville, KY  40422
 
 jennifer.muz...@centre.edu
 http://web.centre.edu/muzyka/
 
 
 
 
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Re: [Jmol-users] Problem with switching to JSMol

2013-02-22 Thread Paul Pillot

Order matters in your js files links
I use the following declaration:
script type=text/javascript src=jmol/JSmol.min.js/script
script type=text/javascript src=jmol/j2s/j2sjmol.js/script
That is with the minified version and without webGL.
Paul

Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :

 Hi, 
 
 I'm trying to switch my JMol applet web page to JSMol - mainly to avoid all 
 the problems related with ever increasing restrictive security policies for 
 Java. I put all the main JSMol files in a folder, j2s in a subfolder, loaded 
 the scripts:
 
 script type=text/javascript src=jsmol/j2s/j2sjmol.js/script
 script type=text/javascript src=jsmol/JSmolCore.js/script
 script type=text/javascript src=jsmol/JSmolApplet.js/script
 script type=text/javascript src=jsmol/JSmolControls.js/script
 script type=text/javascript src=jsmol/JSmolApi.js/script
 script type=text/javascript src=jsmol/JSmolGLmol.js/script
 script type=text/javascript src=jsmol/JSmoljQuery.js/script
 script type=text/javascript src=jsmol/JSmolJSV.js/script
 script type=text/javascript src=jsmol/JSmolThree.js/script
 script type=text/javascript src=jsmol/JSmol.js/script
 
 completed the info section as follows:
 
 var main_info = {
  width: jmolW,
  height: jmolH,
  addSelectionOptions: false,
  color: #00,
  debug: false,
  defaultModel: ,
  memoryLimit: 512,
  readyFunction: null,
  script: ,
  use: HTML5,
  j2sPath: jsmol/j2s,
  serverURL: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;,
  console: myJmol_infodiv,
  scriptCallback: afterscript_callback,
  loadStructCallback: afterload_callback,
  pickCallback: pick_callback,
  src: null,
 }
 
 left the rest of the code unchanged, basically following the instructions 
 found on http://wiki.jmol.org/index.php/JSmol, and now am running the thing 
 on Firefox 18.0.2. I get this error:
 
 TypeError: Jmol._getElement(...).style is undefined
 Jmol._getElement(this, infotablediv).style.display = (tf ? block : 
 none);
 JSmol.js (line 395)
 
 What could be causing this, and what did I forget to do?
 Thank you very much!
 
 Simone
 
 
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Re: [Jmol-users] Transfer show info from JSO to Javascript?

2013-02-22 Thread Paul Pillot

Jmol.evaluate(myJmol1,script(show orientation)) will do !
-Paul

Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit :

 Sorry, I'm just not getting how to do this.
 
 I'd like to get the quaternion info for the current model rotation and 
 manipulate it in Javascript.
 
 I'm using the Jmol Javascript Object.  I'm happily running scripts with 
 something like
 
var script = lots of commands;
Jmol.script (myJmol1, script);
 
 The Jmol command
 
show orientation rotation;
 
 gives me the numbers I want -- in both the Jmol Script Console and in the 
 Java Console.
 
 How do I get these numbers into a Javascript variable?
 
 Something like
 
var q = Jmol.getInfo (myJmol1, show orientation rotation);
 
 is what I'm thinking, but I haven't found a variation that works!
 
 Thanks!
 
 --Dan
 
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Re: [Jmol-users] Signed applet, LoadInline and ajax/db

2013-02-07 Thread Paul Pillot

You can prevent eval() in your code with : document[applet_name].Loadinline(sdf)

Paul

Le 7 févr. 2013 à 17:42, Otis Rothenberger a écrit :

 Quentin,
 
 I'm not fully following your use of pipes, but I think one error is the 
 following:
 
 sdf=sdf.replace(/\|/g,\n|);
 
 I think you need //n not just /n. 
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Feb 7, 2013, at 11:31 AM, Quentin Delettre wrote:
 
 Dear jmol user list,
 
 I have a problem.
 
 In my project, i retrieve molecule in sdf from my database via ajax 
 calls + php. The molecule data is returned as json.
 
 I am doing this because i want to load the molecules only if they are in 
 the browser view, like lazy loading. Ajax calls are made, no problem 
 here and the visibility question is already solved.
 
 So i have the possible case to have multiple applets loaded without 
 content and then when they are displayed to the user, the molecule(s) 
 has to be loaded.
 
 Here is the code :
 
 $.ajax({
 dataType: 'json',
 type: GET,
 url: 
 Routing.generate(myBundle_molstructure_ajax', {
 Id: id
 }),
 success: function (dataStr) {
 // get sdf and prepare
 sdf=|+String(dataStr['sdf']).replace(/\|/g,);
 sdf=sdf.replace(/\r\n/g,|);
 sdf=sdf.replace(/\n/g,|);
 sdf=sdf.replace(/\r/g,|);
 sdf=sdf.replace(/\|/g,\n|);
 
 eval(document. + applet_name + 
 '.LoadInline(\' + sdf + '\);');
 
 }
 });
 
 The error i got is :
 
 SyntaxError: unterminated string literal at
 document.jmol2.LoadInline(
 
 Is there something i can do ?
 I don't think my inline file preparation is wrong but who knows...
 
 Thanks
 
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Re: [Jmol-users] JSmol lite

2013-01-30 Thread Paul Pillot

Minimified and Gzipped, Jsmol is a 700-800kB download.
I am not sure that reducing the download is the way to go in order to improve 
user experience on mobile phones.
I've seen JSmol once on an Iphone and it was really slow. Too slow to call it 
interactive.
Maybe targeting at the graphic performance would be a better goal.
Paul

Le 30 janv. 2013 à 19:59, Michael Evans a écrit :

 Agreed, Otis. I realized after reading your message that a version of JSmol 
 that worked that way would be highly desirable, provided the process of 
 loading files as needed is acceptable from a user experience perspective.
 
 Cheers, Mike
 
 
 ---
 Michael Evans
 Organic Chemistry Graduate Student, Moore Group
 University of Illinois, Urbana-Champaign
 
 
 On Wed, Jan 30, 2013 at 12:54 PM, Otis Rothenberger osrot...@chemagic.com 
 wrote:
 Michael,
 
 I understand your concern, but I'm think about page application development.
 
 If I understand Bob correctly, then functionality would be loaded from server 
 as needed. These loads would be controlled by the page application developer 
 so that it's hidden from users. If that's what Bob is suggesting, I think it 
 would be great.
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Jan 30, 2013, at 1:33 PM, Michael Evans wrote:
 
 Bob,
 I feel like cherry picking functionality to include would present 
 difficulties to users; e.g. I thought JSmol could do x, but it can't!
 
 This is a wild idea, but could the entire command-running apparatus be 
 decoupled from display and mouse actions, with significant savings in code 
 size? I'm imagining something like a kiosk mode, without the machinery of 
 scripting behind it.
 
 I understand this may not be possible; just wanted to throw it out there.
 
 On Wednesday, January 30, 2013, Robert Hanson wrote:
 I'm wondering if we should try to produce a really trimmed-down lite 
 version of Jmol -- a very very minimal core set of functionality that could 
 have better load performance on mobile devices for very basic tasks. 
 
 Maybe just
 
 wireframe
 spacefill
 ballssticks
 no text
 no math (just simple Rasmol-like script commands)
 just XYZ/MOL file reading
 
 (basically a ChemDoodle-HTML5-only-like level of capability)
 
 What would be a reasonable goal for code size?
 
 Suggestions?
 
 (I think I could make it to automatically load additional functionality as 
 needed.)
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
 
 -- 
 
 ---
 Michael Evans
 Organic Chemistry Graduate Student, Moore Group
 University of Illinois, Urbana-Champaign
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Re: [Jmol-users] how do you align center?

2013-01-28 Thread Paul Pillot

Have you tried the css margin: 0 auto; ?
Paul

Le 28 janv. 2013 à 19:52, Jonathan Gough a écrit :

 I can embed a jsmol, using the script nomenclature, but I can't seem to align 
 the embed to the center.  I have tried using allign center and div classes, 
 but nothing.
 
 any suggestions?
 
 Thanks,
 Jonathan
 
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[Jmol-users] bug with signed applet, show history and Jmol.scriptWaitAsArray()

2013-01-27 Thread Paul Pillot

I am converting a former Jmol.js web page to the JOO script library and after 
some testings I've narrowed down the following bug :
- when the signed applet is used and commands are sent with 
Jmol.scriptWaitAsArray(), the aforementioned commands are not displayed by the 
show history command
- when the commands are sent via the Jmol's console or Jmol.script(), they are 
correctly added to the history line
- I've made tests with the pages at St Olaf and found that on the test2.htm 
page, the signed applet is not active (that's the jsmol version instead) and 
that the simple.htm page with the signed applet shows the correct behavior but 
doesn't use the JOO javascript (ie Jmol.js, which was working well for my 
webpage too)

Paul
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Re: [Jmol-users] bug with signed applet, show history and Jmol.scriptWaitAsArray()

2013-01-27 Thread Paul Pillot

Thanks Bob !
I've made more tests using the signed applet on the test2.htm page and found 
the same problem : script sent via Jmol.scriptWait AsArray(jmolApplet0,...) are 
not added to the history, whereas scripts sent through 
Jmol.script(jmolApplet0,...) are.
On the test page simple.html (that uses Jmol.js and the signed applet), scripts 
sent via jmolScriptWaitAsArray(...) are added to the history.
I suspect there is a thread issue involved ?
Paul

Le 27 janv. 2013 à 13:25, Robert Hanson a écrit :

 There's a mistake in the link on that page. You need this after the filename:
 
 ?SIGNEDUSE=JAVA
 
 not just
 
 ?SIGNED
 
 That's because I made the default on that page now to be HTML5, not JAVA.
 
 I'll get that fixed later today.
 
 Bob

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Re: [Jmol-users] bug with signed applet, show history and Jmol.scriptWaitAsArray()

2013-01-27 Thread Paul Pillot

Ok, thanks for the information. I'll rewrite it with the callback pattern.
Paul

Le 27 janv. 2013 à 15:51, Robert Hanson a écrit :

 That is, in fact, the correct  behavior.
 
 In order for a script to appear in the history, it has to have been entered 
 onto the queue, and the scriptWait...() methods do not do that. As much as 
 possible, you should avoid scriptWait methods. Not all script commands can be 
 given that way in JSmol, anyway. Much better to provide a JavaScript command 
 at the end of your script that will act as a callback when the script is 
 completed.
 
 
 
 
 
 On Sun, Jan 27, 2013 at 4:24 PM, Robert Hanson hans...@stolaf.edu wrote:
 I should be able to track that down...
 
 
 On Sun, Jan 27, 2013 at 4:00 PM, Paul Pillot 
 paul.pil...@ac-orleans-tours.fr wrote:
 Thanks Bob !
 I've made more tests using the signed applet on the test2.htm page and found 
 the same problem : script sent via Jmol.scriptWait AsArray(jmolApplet0,...) 
 are not added to the history, whereas scripts sent through 
 Jmol.script(jmolApplet0,...) are.
 On the test page simple.html (that uses Jmol.js and the signed applet), 
 scripts sent via jmolScriptWaitAsArray(...) are added to the history.
 I suspect there is a thread issue involved ?
 Paul
 
 Le 27 janv. 2013 à 13:25, Robert Hanson a écrit :
 
  There's a mistake in the link on that page. You need this after the 
  filename:
 
  ?SIGNEDUSE=JAVA
 
  not just
 
  ?SIGNED
 
  That's because I made the default on that page now to be HTML5, not JAVA.
 
  I'll get that fixed later today.
 
  Bob
 
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 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
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[Jmol-users] bug with Jmol.evaluate and script('show history')

2013-01-27 Thread Paul Pillot

Tests have been done on test2.htm with the unsigned java applet
Jmol.evaluate(jmolApplet0,script('show history')) reports only the first line 
of the history and clears all the following lines (ie : they are not reported 
anymore through the console)

with JSMOL, nothing at all is reported.

Paul

Le 27 janv. 2013 à 15:51, Robert Hanson a écrit :

 That is, in fact, the correct  behavior.
 
 In order for a script to appear in the history, it has to have been entered 
 onto the queue, and the scriptWait...() methods do not do that. As much as 
 possible, you should avoid scriptWait methods. Not all script commands can be 
 given that way in JSmol, anyway. Much better to provide a JavaScript command 
 at the end of your script that will act as a callback when the script is 
 completed.
 
 
 
 
 
 On Sun, Jan 27, 2013 at 4:24 PM, Robert Hanson hans...@stolaf.edu wrote:
 I should be able to track that down...
 
 
 On Sun, Jan 27, 2013 at 4:00 PM, Paul Pillot 
 paul.pil...@ac-orleans-tours.fr wrote:
 Thanks Bob !
 I've made more tests using the signed applet on the test2.htm page and found 
 the same problem : script sent via Jmol.scriptWait AsArray(jmolApplet0,...) 
 are not added to the history, whereas scripts sent through 
 Jmol.script(jmolApplet0,...) are.
 On the test page simple.html (that uses Jmol.js and the signed applet), 
 scripts sent via jmolScriptWaitAsArray(...) are added to the history.
 I suspect there is a thread issue involved ?
 Paul
 
 Le 27 janv. 2013 à 13:25, Robert Hanson a écrit :
 
  There's a mistake in the link on that page. You need this after the 
  filename:
 
  ?SIGNEDUSE=JAVA
 
  not just
 
  ?SIGNED
 
  That's because I made the default on that page now to be HTML5, not JAVA.
 
  I'll get that fixed later today.
 
  Bob
 
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 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
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Re: [Jmol-users] bug with Jmol.evaluate and script('show history')

2013-01-27 Thread Paul Pillot

It's working ! 
Thanks Bob !

Le 27 janv. 2013 à 21:57, Robert Hanson a écrit :

  I see it. The show  history command is supposed to clear out the show 
 history command itself, but only if it is not a top-level command (from the 
 console), but it does more than that if it is part of script(show history). 
 Probably true with all recent versions of Jmol.
 
 Fixed and uploading now.
 

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Re: [Jmol-users] Fwd: Jmol iPad app

2013-01-25 Thread Paul Pillot

I've been asked some time ago, about a facility aimed at students for combining 
a web textbook with the ability to interact with 3D models.
The textbook could be something close to wikipedia, that is articles with links 
making it easy to jump to a glossary for example, or to scientific publications 
related to the subject.
The 3D views in the textbook would lead to a Jmol viewer surrounded by controls 
so that the student could explore by themselves the aforementioned model, 
searching for interesting features.

All of this could be done through webpages especially now that we have Jsmol.
But if an app is created for iPads (or other tablets as as Otis points it, 
Apple policies regarding iOS and apps are more than questionable), it could be 
a good idea to have the user clicking on a link (this could be a thumbnail or 
anything clickable probably through a custom urlscheme) from an article, and 
the app opening with the corresponding view of the 3D model + commands. I can 
see what it would look like if there is only simple interactions (a button 
throwing a script). What I can't see is how we can make more complex widgets 
that for example poll informations from the applet and create a context 
accordingly (for example an interactive sequence viewer, etc...) without 
reinventing a whole web-browser !
The idea of a repertoire of Jmol slides opening at startup looks great

Paul

Le 24 janv. 2013 à 16:39, Bob Hanson a écrit :

 
 Begin forwarded message:
 
 From: Robert Hanson hans...@stolaf.edu
 Date: January 24, 2013 4:14:54 PM GMT+02:00
 To: undisclosed-recipients:;
 Subject: Jmol iPad app
 
 Dear Jmol users,
 
 The Jmol iPad app. The  obvious next step, right? So, I'd like to start a 
 discussion with Jmol users and Jmol page developers. 
 
 IF we were to work on an iPad app, what would it take to make it the killer 
 app that would equal Jmol as the killer applet.? What is it that makes 
 Jmol/JSmol unique as an applet/JavaScript library? 
 
 Some ideas:
 
 -- scriptability - One of Jmol's key features is its high-level scripting 
 language that lets both web developers and (knowledgeable) web users 
 interact with it in ways that Jmol developers ourselves haven't  
 conceptualized. 
 
 -- adaptability - Web page developers can put the applet in a context of 
 their own choosing, with all sorts of interesting content around the applet 
 that makes this particular page for a page visitor a particularly 
 interesting and unique interactive experience.
 
 Of these two, the first is probably very easy to implement in a Jmol app.  
 What about the second? 
 
 My thinking goes like this: There are three groups:
 
 -- Jmol code developers (meaning those of us writing the Java code)
 -- Jmol page developers (those using Jmol for their own creative ends using 
 the code and interfaces developed by the Jmol code developers)
 -- Jmol users (those who visit the pages created by the Jmol page developers)
 
 If you think about it, that second category is what makes Jmol unique. There 
 are programs out there like pyMol and Mercury, and others that are created 
 by code developers and  used by users. But what other programs involve the 
 middle category? I think of Adobe Flash as something like that. Is that it? 
 Jmol is more like Flash than it is like pyMol? Jmol provides the technology 
 that page developers can use to design a unique experience for their page's 
 visitors. This is what makes Jmol quite different from, say, a JavaScript 
 library that allows one to pop up a 3D model on a page and pretty much 
 leaves it at that. That's what the combination of controls and high-level 
 scripting gets us. Right?
 
 It seems to me, that if a Jmol app were to be valuable, it would still 
 involve this triad of involvement. Wouldn't it be a waste of time to develop 
 just another molecule viewer even if it is Jmol? That would be more like 
 morphing the Jmol application into an iPad app, not the Jmol applet.
 
 But how would we maintain that middle tier? 
 
 One idea: The Jmol app by itself does little. But what it does do is 
 interact with a cloud-based server (or perhaps any web site?) to pull 
 context down and surround the viewer window with that context. So what a 
 Jmol context developer (I can't think of the analogy in terms of iPad 
 apps, because I don't think there is this category yet) would do would be to 
 develop an actual web page with an actual computer using a standard browser 
 and then through some sort of registered process upload, perhaps, a link to 
 that page along with a thumbnail image and a set of searchable keywords or 
 abstract. While that page could be viewed on the browser, some version of it 
 could also be viewed within the Jmol app. When the Jmol app is opened, it 
 would be like getting an index to all the Jmol pages in existence -- those 
 adapted to this iPad idea. The user would  select the [what? -- applet? 
 (does sound about right...)] of choice and off they go. That

Re: [Jmol-users] JSmol version issue

2013-01-16 Thread Paul Pillot

Otis,
web inspector on safari have a panel to show this activity (network) : which 
files are indeed loaded, which others are loaded from cache
you'll have a very informative timeline as well
-Paul

Le 16 janv. 2013 à 16:31, Otis Rothenberger a écrit :

 Phil,
 
 Still like clockwork - 40 seconds.
 
 Bob, I think I need some conceptual help with how JSmol works. If I load a 
 page and do a MEP, I understand that files are loaded from the server during 
 this process. Now assuming that all of these files loaded into cache, on a 
 second call to MEP, is there any sever activity?
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Jan 16, 2013, at 9:54 AM, Philip Bays wrote:
 
 Otis:
 Does it make any difference if you turn on private browsing in Safari?
 
 
 
 Philip Bays
 Saint Mary's College
 Notre Dame, IN 46556
 
 Sent from my iPhone
 
 
 
 On Jan 16, 2013, at 9:42 AM, Otis Rothenberger osrot...@chemagic.com wrote:
 
 Thanks Nick,
 
 I'm in Florida, CheMagic is in North Carolina, and ISU is in Illinois, so 
 that's not the problem.
 
 This is frustrating. I just don't get it. Nevertheless, I guess I should 
 put 13.1.12_dev on CheMagic just to make sure it's not a server issue.
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Jan 16, 2013, at 9:02 AM, Greeves, Nick wrote:
 
 Hi Otis,
 From the UK and clearing the cache before each test I get 11-13 sec for 
 ISU and 8-9 sec for Chemagic.
 
 Mac OS 10.8.2 Safari 6.0.2
 
 Could it be that you are physically closer to the Chemagic server on your 
 network?
 
 All the best
 Nick
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 On 16 Jan 2013, at 13:26, jmol-users-requ...@lists.sourceforge.net
  wrote:
 
 Message: 1
 Date: Tue, 15 Jan 2013 22:52:47 -0500
 From: Otis Rothenberger osrot...@chemagic.com
 Subject: Re: [Jmol-users] JSmol version issue
 To: jmol-users@lists.sourceforge.net
 Message-ID: 5aab83e9-ef53-421d-bd50-c30028645...@chemagic.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Thanks Jeff,
 
 I don't get it. I'm consistently getting 40 seconds on Safari (6.0.2) Mac 
 10.7.5.
 
 I wonder if I have a file corrupted in cache. Wait...
 
 I have a little portable Mac Air. It's about 15 seconds at ISU and 3 
 seconds for CheMagic.
 
 Another thing is that the original page load is REALLY long for the ISU 
 server on both Macs.
 
 Do double precision numbers have any bandwidth issues that might cause an 
 ISP variable issue?
 
 Otis
 
 
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[Jmol-users] calculate partialcharge broken ?

2013-01-04 Thread Paul Pillot

Apparently the command calculate partialcharge doesn't work in v13.1.11 and 
causes the applet to stop working

To reproduce the bug :
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm
Click Load MOL by NAME
Load the default model
Type in the command slot : calculate partialcharge

the java console gives back the following message : 
script 4 started
0 SMARTS matches used
QueueThread1_41 exception java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

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Re: [Jmol-users] gzip pdb file in JSmol

2012-12-12 Thread Paul Pillot

Hi,
do you have a pointer to this file, so that we can have a look at the headers ?
Does Safari on your Mac load this gzipped file well ?
Paul

Le 12 déc. 2012 à 19:02, Wayne Decatur a écrit :

 Hi,
 I have JSmol opening a gzipped pdb file served from a web server on a Mac. 
 All is well there. However, the same gzipped file from the same web server 
 source for JSmol gives an unknown type error message on an iPad where the 
 owner even set the browser settings all to factory. The same iPad will open 
 the gzipped water molecule in JSmol from Bob's test2.html page via his web 
 server.
 Anybody seen anything like this?
 Thanks,
 Wayne
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[Jmol-users] testing needed for xml loading

2012-12-10 Thread Paul Pillot




On Chrome MacOSX.6
no error with vasp.xml and water.xodydata. 
estron.cml reports the following error :
FileManager.getAtomSetCollectionFromFile(estron.cml)
starting HoverWatcher_7
FileManager opening http://chemapps.stolaf.edu/jmol/jsmol/estron.cml
The Resolver thinks XmlCml
call loadScript org\jmol\adapter\readers\xml\XmlCmlReader.js
call loadScript org\jmol\adapter\readers\cifpdb\CifReader.js
call loadScript org\jmol\api\JmolLineReader.js -- required by 
org.jmol.adapter.readers.cifpdb.CifReader
call loadScript org\jmol\adapter\smarter\Structure.js
Time for openFile(estron.cml): 2361 ms
File Error:Error reading XML: Cannot call method 'clear' of null
for file http://chemapps.stolaf.edu/jmol/jsmol/estron.cml
type xml
starting HoverWatcher_8
script ERROR: Error reading XML: Cannot call method 'clear' of null
for file http://chemapps.stolaf.edu/jmol/jsmol/estron.cml
type xml

load  estron.cml 
Script completed
Jmol script terminated

Paul

PS: (this may help) jQuery offers possibilities for parsing XML documents with 
the $() function.
Here is a code example I've made to fetch pubmed abstracts from a PDB ID :
$.ajax({
  url: 
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi;,
  data: {
db: pubmed,
id: pId,
retmode: xml,
rettype: abstract
  },
  success: function(t){
var $xml = $(t);
var txt = '';
var pmc = $xml.find(ArticleId[IdType='pmc']).text();
var volume = $xml.find(Volume).text();
var revue = $xml.find(Title).text();
var pages = $xml.find(MedlinePgn).text();
var annee = $xml.find(Year:first).text();
var doi = $xml.find(ArticleId[IdType='doi']).text();
var abstract = $xml.find(AbstractText).text();

txt += 'br /span class=label label-infoin/span 
'+revue+' '+annee+' n°'+volume+ ' p'+pages+' ';
...
});
Le 10 déc. 2012 à 13:22, Robert Hanson a écrit :

 I'd appreciate people testing 
 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5 for those top 
 middle links involving loading of XML files (vasp.xml, estron.cml, and 
 water.xodydata). This uses the browser's own HTML document object model to 
 parse the XML files. It seems to be working on Firefox and MSIE under 
 Windows. 
 
 If you get a file loading error, please click show to see the console, clip 
 that, and send it to me off-list.
 
 I know about the this.atts is null error that arises when you first load 
 vasp.xml and then load estron.cml. Trying to track that one down.
 
 Thanks,
 
 Bob
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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Re: [Jmol-users] testing needed for xml loading

2012-12-10 Thread Paul Pillot

That's interesting ! I've made further testing and found out that the sequence 
of file loading can trigger an error with the cml file !
- reloading the page and :
1. load estron.cml
2. load vasp.xml
3. load water.xodydata
causes no error

- reloading the page and :
1. load vasp.xml or load water.xodydata
2 load estron.cml
triggers the error reading XML message

That's MacOs 10.6.8 with Chrome 23.0.1271.95

Le 10 déc. 2012 à 14:16, Otis Rothenberger a écrit :

 Paul,
 
 That loads for me on Mac 10.7.5 with Chrome 23.0.1271.95.
 
 Otis
 
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Dec 10, 2012, at 7:58 AM, Paul Pillot wrote:
 
 
 
 
 On Chrome MacOSX.6
 no error with vasp.xml and water.xodydata. 
 estron.cml reports the following error :
 FileManager.getAtomSetCollectionFromFile(estron.cml)
 starting HoverWatcher_7
 FileManager opening http://chemapps.stolaf.edu/jmol/jsmol/estron.cml
 The Resolver thinks XmlCml
 call loadScript org\jmol\adapter\readers\xml\XmlCmlReader.js
 call loadScript org\jmol\adapter\readers\cifpdb\CifReader.js
 call loadScript org\jmol\api\JmolLineReader.js -- required by 
 org.jmol.adapter.readers.cifpdb.CifReader
 call loadScript org\jmol\adapter\smarter\Structure.js
 Time for openFile(estron.cml): 2361 ms
 File Error:Error reading XML: Cannot call method 'clear' of null
 for file http://chemapps.stolaf.edu/jmol/jsmol/estron.cml
 type xml
 starting HoverWatcher_8
 script ERROR: Error reading XML: Cannot call method 'clear' of null
 for file http://chemapps.stolaf.edu/jmol/jsmol/estron.cml
 type xml
 
 load  estron.cml 
 Script completed
 Jmol script terminated
 
 Paul
 
 PS: (this may help) jQuery offers possibilities for parsing XML documents 
 with the $() function.
 Here is a code example I've made to fetch pubmed abstracts from a PDB ID :
 $.ajax({
url: 
 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi;,
data: {
  db: pubmed,
  id: pId,
  retmode: xml,
  rettype: abstract
},
success: function(t){
  var $xml = $(t);
  var txt = '';
  var pmc = $xml.find(ArticleId[IdType='pmc']).text();
  var volume = $xml.find(Volume).text();
  var revue = $xml.find(Title).text();
  var pages = $xml.find(MedlinePgn).text();
  var annee = $xml.find(Year:first).text();
  var doi = $xml.find(ArticleId[IdType='doi']).text();
  var abstract = $xml.find(AbstractText).text();
  
  txt += 'br /span class=label label-infoin/span 
 '+revue+' '+annee+' n°'+volume+ ' p'+pages+' ';
  ...
 });
 Le 10 déc. 2012 à 13:22, Robert Hanson a écrit :
 
 I'd appreciate people testing 
 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5 for those top 
 middle links involving loading of XML files (vasp.xml, estron.cml, and 
 water.xodydata). This uses the browser's own HTML document object model to 
 parse the XML files. It seems to be working on Firefox and MSIE under 
 Windows. 
 
 If you get a file loading error, please click show to see the console, 
 clip that, and send it to me off-list.
 
 I know about the this.atts is null error that arises when you first load 
 vasp.xml and then load estron.cml. Trying to track that one down.
 
 Thanks,
 
 Bob
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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Re: [Jmol-users] Ketcher

2012-11-30 Thread Paul Pillot

prototypejs defines a global $() object as well as jquery.
ketcher relies on prototypejs and jsmol on jquery
a conflict probably lies there
-Paul

Le 30 nov. 2012 à 16:30, Robert Hanson a écrit :

 It would be interesting to know more about those code collisions. We don't 
 want to have to use iFrames. I'm aware of several issues with Java2Script, 
 and I've probably introduced a few with JSmol as well. 
 
 Otis, could you do us a favor and combine these in one JS file?
 
 script type=text/javascript src=prototype-min.js/script
 script type=text/javascript src=raphael.js/script
 script type=text/javascript src=base64.js/script
 script type=text/javascript src=util/common.js/script
 script type=text/javascript src=util/vec2.js/script
 script type=text/javascript src=util/set.js/script
 script type=text/javascript src=util/map.js/script
 script type=text/javascript src=util/pool.js/script
 script type=text/javascript src=chem/element.js/script
 script type=text/javascript src=chem/struct.js/script
 script type=text/javascript src=chem/molfile.js/script
 script type=text/javascript src=chem/sgroup.js/script
 script type=text/javascript src=chem/struct_valence.js/script
 script type=text/javascript src=chem/dfs.js/script
 script type=text/javascript src=chem/cis_trans.js/script
 script type=text/javascript src=chem/stereocenters.js/script
 script type=text/javascript src=chem/smiles.js/script
 script type=text/javascript src=rnd/events.js/script
 script type=text/javascript src=rnd/visel.js/script
 script type=text/javascript src=rnd/restruct.js/script
 script type=text/javascript 
 src=rnd/restruct_rendering.js/script
 script type=text/javascript src=rnd/render.js/script
 script type=text/javascript src=rnd/editor.js/script
 script type=text/javascript src=rnd/elem_table.js/script
 script type=text/javascript src=rnd/rgroup_table.js/script
 script type=text/javascript src=ui/ui.js/script
 script type=text/javascript src=ui/actions.js/script
 script type=text/javascript src=reaxys/reaxys.js/script
 script type=text/javascript src=ketcher.js/script
 
 
 
 
 
 
 On Fri, Nov 30, 2012 at 7:54 AM, Otis Rothenberger osrot...@chemagic.com 
 wrote:
 On Safari, things get real slow if I have the error console on. When I turn 
 it off, JSmol response quickly.
 
 I had a real problem trying to make these two applications work on the same 
 page. I kept getting apparent code collisions with the two applications in 
 the same page. Consequently, I put Ketcher in its own iframe. I also use 
 absolute positioning of all containers. This was probably asking for cross 
 browser/platform issues. I guess it could also affect response.
 
 I'll keep working on it.
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Nov 30, 2012, at 8:11 AM, Mikko Rantalainen wrote:
 
  Otis Rothenberger, 2012-11-30 06:25 (Europe/Helsinki):
  OK, here you go:
  http://chemagic.com/draw.htm
 
  It works on Mac FF, Chrome, and Safari (including iPad). I'm interested
  in how it works on Windows.
 
  The Get InChiKey button is there because we're using it to grade
  quizzes. Both buttons use Resolver, so clicking the Get InChIKey button
  is a quick way to see if Resolver is up.
 
  Very nice demo!
 
  Is it just me or is this super-heavy in CPU usage for anybody else? The
  Jmol view is barely usable (framerate is probably around 1-2 fps) on
  dual core 3GHz desktop computer running Ubuntu 12.04 LTS 64 bit and
  Firefox 17.0.
 
  --
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 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
 --
 Keep yourself connected to Go Parallel: 
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[Jmol-users] JSmol -- Are we done? Gestures

2012-11-26 Thread Paul Pillot

So many improvements, it's hard to keep pace.

I've just (re)tried with an iPad and found out that gestures now work : pinch 
to zoom, two fingers for a translation.
There is even a support for picking measurements through double tap.
This is fabulous !

Measurements are tricky : it's difficult to know if an atom has been properly 
clicked on as there is no possibility to hover on a touch interface.
I don't know how zoom works : it appears that when a pinch or pinch out has 
been initiated, as long as both fingers are kept on the screen, the zooming is 
still processing (there might be a delay due to the refresh rate, but at least 
it gave me that impression). I assumed that instead the scaling would follow 
the tips of my fingers (that is, if I have both fingers on two atoms and I 
pinch, the molecule would be shrinked until the two atoms fit between my 
fingers). Does it make sense ?

-Paul
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Re: [Jmol-users] minimization using GPU

2012-11-25 Thread Paul Pillot

Apparently WebCL is the technology involved here, but it is not supported yet 
natively by any browser. Extensions exist for firefox and webkit.
-Paul

Le 25 nov. 2012 à 18:05, Dan Damelin a écrit :

 Hi Bob,
 
 At the moment we don't have any free cycles in our development group for 
 something not in the immediate horizon. Our current focus is on porting our 
 2D molecular dynamics engine to HTML5/JS/. However, at some point in the 
 future if we decide to develop an activity that would require this we'll 
 certainly be interested in working on it or at least gauging the feasibility.
 
 The work you and other Jmol developers have done so far is always amazing and 
 well appreciated.
 
 -Dan
 
 On Nov 24, 2012, at - November 24 - 11:37 PM, 
 jmol-users-requ...@lists.sourceforge.net wrote:
 
 Definitely worth a try. It's quite a bit of code. I don't have any idea how
 to do it in the GPU.
 
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Re: [Jmol-users] JSmol -- Are we done?

2012-11-24 Thread Paul Pillot

The zip file available is apparently an older version (from the 11/13). There 
might be some caching problem there, preventing from downloading the latest 
version ?

I don't know if it's time to discuss this yet, but I have some comments about 
JSmol:
- speed performance: a colleague of mine reported poor performance using both 
his computer and his smartphone. I can't complain on my computer except for big 
structures. On iPad, caffeine is fine, but bigger biological structures are 
harder to rotate. On iPhone (v4) it looks very slow (even Caffeine).
Using Chrome's timeline tools I tried to have measures of JSmol performances :
- JSmol HTML5 only, caffeine, antialias on: 28 FPS
- JSmol HTML5 only, caffeine antialias off : 60 FPS
- JSmol HTML5 only, 1HBA (balls and sticks) antialias on: 6 FPS
- JSmol HTML5 only, 1HBA (balls and sticks) antialias off: 14 FPS
- JSmol HTML5 only, 1HBA (cartoons) antialias on: 6 FPS
- JSmol HTML5 only, 1HBA (cartoons) antialias off: 14 FPS
- JSmol HTML5 WebGL, caffeine, antialias on: 60 FPS
- JSmol HTML5 WebGL, 1HBA (balls and sticks) antialias on: 3 FPS
- JSmol HTML5 WebGL, 1HBA (cartoons) antialias on: 40 FPS
WebGL improves performance a lot, except when there is a large number of atoms 
to display.
I was wondering about the use of setTimeout() instead of 
requestAnimationFrame() in the HTML5 only JSmol version (whereas the WebGL 
version uses requestAnimationFrame). Does it make a difference ?

- gesture support: at present on an iPad I can only rotate the model. There is 
no zooming, no measures after a double tap

Paul
 
Le 24 nov. 2012 à 19:43, Robert Hanson a écrit :

 I think we are close to saying that that conversion from Java to JavaScript 
 is done. What am I forgetting?
 
 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
 
 -- all links working?
 -- working on all browsers?
 -- mouse actions are working?
 -- all file types loading?
 
 Is that everything? Can we say it is ready for release?
 
 known issues:
 
 -- no support for width/height expressed in %
 -- no popup menu
 -- no CONSOLE command, but Jmol.showInfo(applet,true/false) works, and you 
 can enter commands either using the command input box or using  in the 
 Search text box.
 -- could be issues loading some less-common binary file types for surfaces in 
 particular. 
 
 That's all I can think of. 
 
 Bob

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[Jmol-users] JSmol - three months in... and compression

2012-11-21 Thread Paul Pillot

I've tried minifying JSmol (yes, again), with the new version. After gziping by 
the server, the results are :
- 720kB with WebGL
- 666kB without WebGL
(including 4kB just for the HTML page)
(I don't have the extra download of 40+ files, as I had previously so the 
minifying process works as expected.)

For information, without minifying and with just server side compression of 
text files, test2.htm is a 862kB transfer.
So the key here is gziping (at present without any kind of compression 
test2.htm is a 4.09MB transfer) and minifying doesn't hurt

Paul


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Re: [Jmol-users] two JSmols in the page

2012-11-20 Thread Paul Pillot

Hi Angel,
have you tried plain test2.htm first ? I encountered a problem with the zip 
distribution at some point yesterday and these error messages look familiar.
Paul

Le 20 nov. 2012 à 21:05, Angel Herráez a écrit :

 Dear all,
 
 I'm trying a page with two Jmols using Jmol-JSO. My code is like this:
 
 var myJmol1,myJmol2;
 var myInfo = {
   height: '50%',
   width: '100%',
   jarFile: JmolApplet.jar,
   jarPath: JmolPath,
   j2sPath: JmolPath + /j2s,
   use: 'HTML5',
   debug: false
 };
 myJmol1 = Jmol.getApplet(myJmol1, myInfo); 
 myJmol2 = Jmol.getApplet(myJmol2, myInfo); 
 Jmol.script(myJmol1, 'load maltosa.sdf;' );
 Jmol.script(myJmol2, 'load celobiosa.sdf;' );
 
 When I set it to use the Java applet (use: 'Java HTML5'), both are displayed.
 But when I try to use HTML5 only, I get no display, just the two yellow 
 topbars
 
 Jmol._Canvas2D (JSmol) myJmol1[x]
 Jmol._Canvas2D (JSmol) myJmol2[x]
 
 and an error in the Info console (which output goes into the page in this 
 case)
   
 loadScript ../j2s/java/package.js
 Application loaded.
 loadScript ../j2s/core.z.js --- ClazzNode
 loadScript ../j2s/core.z.js --- w3c script failed
 
 I'm using a recent set of JSmol files (obtained 2 days ago). I am trying to 
 download the latest now, but is it not easy, so I thought first to ask if 
 this ticks 
 some ideas.
 
 Thanks
 
 
 
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Re: [Jmol-users] My trial wit JSmol

2012-11-19 Thread Paul Pillot


Le 16 nov. 2012 à 18:04, Robert Hanson a écrit :

 
 Ultimately, I think we will still end up with the full load of 600 or so .js 
 files. I know that sounds ridiculous, but really what it means is that there 
 are so many options in Jmol, that defining or implementing all of them at 
 once is not feasible. Instead, little bits of Jmol will fly over AJAX as 
 needed no matter what the installation involves. About 300 of those files 
 will never load and are not needed because their classes are present in 
 j2s/java/core.z.js, which is loaded initially. Those are basically what it 
 takes to deliver a simple model of caffeine. But I'm not sure it makes any 
 sense to selectively remove those from the distribution. (What do others 
 think?) 
At the moment, after cafeine is loaded, when I load 1crn.pdb, an extra 40 files 
are requested before the pdb file. I am currently on a rather slow internet 
connection and each file request has a latency of about 150ms according to 
chrome dev tools. Thus, delivering those 40 files as one package would 
certainly speed the process noticeably at least when cache is empty.
As for the 300 files never loaded, I am not sure I get your point correctly : 
do you mean that those files are in the distribution but are never loaded ?
If that's the case, I don't think it really matters. I suppose that at some 
stage we might move to a developer version with all the plain javascript files, 
to a deployment version with minimified packaged files (maybe served from a CDN 
service if one is available to our purposes). For now we only have the 
developer version.
 
 Jmol itself already does this modular packaging to a certain extent, 
 delivering a 1 Mb chunk initially, then smaller chunks. This class-on-demand 
 scheme with JSmol is better in some ways, as all the additional files are 
 relatively small, and the core package can be kept reasonably small. (3 Mb). 
 
 I would be very interested in having some help on the following issues:
 
 -- pop-up menu -- how to implement? We can easily get a structured list of 
 what's on the menu, the question is how to present it in HTML5. 
jqueryui is a framework that comes with a menu widget : 
http://jqueryui.com/menu/
it's another 40kB + 20kB css...
 
 -- console -- how to implement a simple pop-up console, if people feel that 
 is important.
jqueryui has a dialog widget which could be suitable to this end : 
http://jqueryui.com/dialog/#default
 
 -- PROMPT command. The simple question/answer one is easy, but Jmol allows a 
 richer context, with button lists and such. How should we implement this in 
 JSmol?
 
maybe another dialog widget ?

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[Jmol-users] JSmol gz compression

2012-11-19 Thread Paul Pillot

I've enabled Apache mod-deflate on my local machine.
It compresses all html/js/css files. I have also minimified, thanks to 
uglifyjs2, core.z.js (down to a 2.6MB file)

Loading the test2.htm page on my local server resulted in a 2.9MB transfer, 
whereas the same page results in a 4.09MB transfer.
The main issue there is that all files are compressed by mod-deflate except 
core.z.js. It means that this file is served as a 2.6MB file (instead of 540kB 
if properly gziped)
Looking at the headers from the server, it appears that Apache considers this 
file as already being compressed.
I suspect that changing the filename to plain core.js would allow it to be 
properly processed.

Paul
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Re: [Jmol-users] JSmol gz compression

2012-11-19 Thread Paul Pillot

It works and caffeine is loaded after a 871kB download ! core.js is sent as a 
564kB file.
Surprisingly 43 js files are loaded after core.js (shaperenderer.js, 
ballrenderer.js, deflate.js, gzipheaders.js to name a few). Those files are not 
loaded on the test page delivered by the chemapps... server. Something might 
have happened somewhere in the ugglifying process ?

Still, a remaining 307kB might be reduced by compressing the main libraries 
(JSmolApi.js and the like) and downloading jquery through google api cdn.

Paul

Le 19 nov. 2012 à 19:02, Robert Hanson a écrit :

 go ahead and change that name. It is referenced in j2s/java/package.js
 

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[Jmol-users] JSmol compression techniques

2012-11-19 Thread Paul Pillot

So... by combining all the JSmol.js files (including the huge three.js
library for webGL) in a minimified version, I got a 418kB file which gziped as
a 90kB file.
accessing jquery from CDN, lead to download a 33kB compressed file and core.js
is still compressed accounting for 560kB
test2.htm loaded in a 772kB transfer after 54 requests.
As I mentioned previously there is a bunch of extra files which I think could
be related to a difference of version between the jsmol zip file I downloaded
(version 11/13/2012) and the actual online version (11/18/2012). I presume that
without these extra requests the initial load would amount to 700kB. Bob, can
this be fairly compared with the 1MB JmolApplet0.jar file ?

For information, here is how I processed :
- fetching JQuery from CDN :
script
src=//ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js/script
- minimifying JS files using uglifyjs2 (after installing node and the uglifyjs2
package through npm) https://github.com/mishoo/UglifyJS2
- core.z.js :
uglifyjs2 core.z.js -o core.js --compress
- JSmolxxx.js files
uglifyjs2 JSmolCore.js JSmolApplet.js JSmolApi.js
JSmolThree.js JSmolGLmol.js j2s/j2sjmol.js JSmol.js -o JSmol.min.js --compress
unsafe=false
(using --compress without specifying the unsafe=false argument breaks this code)
- changing the script tags :
script type=text/javascript src=JSmol.min.js/script

For server side js files compression I edited the httpd.conf file of my Apache
server in accordance with this tutorial :
http://www.techiepark.com/tutorials/how-to-enable-gzip-compression-in-apache-server-to-speed-up-website/
mol and pdb files also benefit from this setting

Paul

Le 19 nov. 2012 à 20:52, Paul Pillot a écrit :

It works and caffeine is loaded after a 871kB download ! core.js is sent as a
564kB file.
Surprisingly 43 js files are loaded after core.js (shaperenderer.js,
ballrenderer.js, deflate.js, gzipheaders.js to name a few). Those files are
not loaded on the test page delivered by the chemapps... server. Something
might have happened somewhere in the ugglifying process ?

Still, a remaining 307kB might be reduced by compressing the main libraries
(JSmolApi.js and the like) and downloading jquery through google api cdn.

Paul

Le 19 nov. 2012 à 19:02, Robert Hanson a écrit :

go ahead and change that name. It is referenced in j2s/java/package.js

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Re: [Jmol-users] JSmol compression techniques

2012-11-19 Thread Paul Pillot

Apparently there could be some issues with some browsers.
This blog post
http://rickchristie.com/blog/2010/note/gzip-in-safari-doesnt-work-not/ states
it happens with safari 4.0 unless the js file extension is changed from .js.gz
to .jgz
I had a look at many websites about JS optimization and I always read about
server side proper configuration. Plus, when you download a js library, there
is always a minified version ready for production sites but I can't remember
seeing a gziped version of the library (which I think would exist if it would
work out of the box). In one case (TinyMCE), I remember of an extra php file to
take care of compressing js and css on the fly.
It's not my area of expertise, and I agree that if we can be sure this strategy
is working, we should implement it (and we don't have to care for all browsers
as, for example, jsmol relies on canvas for rendering, it's not necessary to
achieve compatibility with IE9). Maybe testing is required.
Paul

Le 19 nov. 2012 à 22:57, Evans, Michael James a écrit :

Bob,
Yes, you should try it! :-) Modern browsers know how to handle gzip files.
Think of it this way: if you open an MP3 file in your browser, the browser
plays it, right? The MP3 doesn't open in another application unless you
explicitly tell it to or download it. In similar fashion, gzip files are
handled by the browser too. They just get unzipped and the unzipped file gets
pulled in and processed by the browser.

Cheers, Mike

On Nov 19, 2012, at 3:51 PM, Robert Hanson hans...@stolaf.edu wrote:

On Mon, Nov 19, 2012 at 3:41 PM, Paul Pillot
paul.pil...@ac-orleans-tours.fr wrote:
So... by combining all the JSmol.js files (including the huge three.js
library for webGL) in a minimified version, I got a 418kB file which gziped
as a 90kB file.
accessing jquery from CDN, lead to download a 33kB compressed file and
core.js is still compressed accounting for 560kB
test2.htm loaded in a 772kB transfer after 54 requests.
As I mentioned previously there is a bunch of extra files which I think
could be related to a difference of version between the jsmol zip file I
downloaded (version 11/13/2012) and the actual online version (11/18/2012).
I presume that without these extra requests the initial load would amount to
700kB. Bob, can this be fairly compared with the 1MB JmolApplet0.jar file ?

Quite possibly. You should be able to use the files in
http://chemapp.stolaf.edu/jmol/jsmol.zip and have NO org/jmol downloads and
NO java/ downloads for anything that is not biological. If you see any
additional files, then something is wrong with the compression. Function
names have changed, for example. But, yes, I would say 1 MB is our target,
since that is the size of JmolApplet0.jar.

I don't understand the gzip business. Do all browsers now accept gzipped .js
files? How does that work?

Bob

For information, here is how I processed :
- fetching JQuery from CDN :
script
src=//ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js/script
- minimifying JS files using uglifyjs2 (after installing node and the
uglifyjs2 package through npm) https://github.com/mishoo/UglifyJS2
- core.z.js :
uglifyjs2 core.z.js -o core.js --compress
- JSmolxxx.js files
uglifyjs2 JSmolCore.js JSmolApplet.js JSmolApi.js JSmolThree.js
JSmolGLmol.js j2s/j2sjmol.js JSmol.js -o JSmol.min.js --compress unsafe=false
(using --compress without specifying the unsafe=false argument breaks this
code)
- changing the script tags :
script type=text/javascript src=JSmol.min.js/script

For server side js files compression I edited the httpd.conf file of my
Apache server in accordance with this tutorial :
http://www.techiepark.com/tutorials/how-to-enable-gzip-compression-in-apache-server-to-speed-up-website/
mol and pdb files also benefit from this setting

Paul

Le 19 nov. 2012 à 20:52, Paul Pillot a écrit :

It works and caffeine is loaded after a 871kB download ! core.js is sent as
a 564kB file.
Surprisingly 43 js files are loaded after core.js (shaperenderer.js,
ballrenderer.js, deflate.js, gzipheaders.js to name a few). Those files are
not loaded on the test page delivered by the chemapps... server. Something
might have happened somewhere in the ugglifying process ?

Still, a remaining 307kB might be reduced by compressing the main libraries
(JSmolApi.js and the like) and downloading jquery through google api cdn.

Paul

Le 19 nov. 2012 à 19:02, Robert Hanson a écrit :

go ahead and change that name. It is referenced in j2s/java/package.js

Re: [Jmol-users] JSmol tweaks

2012-11-18 Thread Paul Pillot

My mistake : variables names are changed to reduced ones (one letter), but this 
is not the case for objects names (such as Long, Clazz,... etc...) nor for 
their methods.
Paul

Le 18 nov. 2012 à 23:28, Paul Pillot a écrit :

 For information,
 I've just tried to minimify the jsmocore.z.js file using the uglifyjs library 
 running on node.js
 With default parameters It shrinked the file from 3.4 to 2.5 Mo (-26%) which 
 is less than what I expected...
 I replaced the original file by its compressed version and it seemed to work  
 exactly as expected (I cleaned the cache before and made sure the compressed 
 file is indeed loaded).
 Looking at the code showed that variable names were kept identical, as well 
 as some comments
 Paul
 
 Le 13 nov. 2012 à 20:31, Robert Hanson a écrit :
 
 
 
 JSmolThree.js and JSmolGLmol.js are only necessary if you are using the 
 WebGL version (which currently is only partially working). 
 
 None of these are compressed. If someone wants to do that and test that or 
 send them back to me, that would be great. The main file that might benefit 
 from compression would be j2s/java/core.z.js
 
 Bob
 

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Re: [Jmol-users] JSmol tweaks

2012-11-18 Thread Paul Pillot

I've just tried the Closure compiler (jar application version) with the same 
jsmolcore.z.js file
default options reduce the size to 2.4 Mo which is about the same amount of 
compression as uglify.js.
there is an advanced compression setting allowing for reducing functions names. 
Setting this flag leads to a 1.6MB file
But, unsurprisingly, it also breaks the code as other scripts calls to this 
script can't be processed. To achieve that, all the files should
be processed and compressed simultaneously by the compiler (which I haven't yet 
found out how to do).
It might be of further interest to know that this 1.6MB file can be gziped to a 
500kB file. So, minimification + gzip compression could reduce the load by 7 
(3.4MB0.5MB).
Paul

Le 18 nov. 2012 à 23:50, Paul Pillot a écrit :

 For information,
 I've just tried to minimify the jsmocore.z.js file using the uglifyjs 
 library running on node.js
 With default parameters It shrinked the file from 3.4 to 2.5 Mo (-26%) which 
 is less than what I expected...
 I replaced the original file by its compressed version and it seemed to work 
  exactly as expected (I cleaned the cache before and made sure the 
 compressed file is indeed loaded).
 Looking at the code showed that variable names were kept identical, as well 
 as some comments
 Paul
 
 Le 13 nov. 2012 à 20:31, Robert Hanson a écrit :
 
 
 
 JSmolThree.js and JSmolGLmol.js are only necessary if you are using the 
 WebGL version (which currently is only partially working). 
 
 None of these are compressed. If someone wants to do that and test that or 
 send them back to me, that would be great. The main file that might benefit 
 from compression would be j2s/java/core.z.js
 
 Bob
 

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Re: [Jmol-users] JSmol tweaks

2012-11-18 Thread Paul Pillot

Apparently, one can set up the server to choose which version of the file (gzip 
or plain) to deliver accordingly with the headers sent by the client's browser.
Apache mod-gzip + caching seems to achieve similar results.

Paul


Le 19 nov. 2012 à 01:12, Evans, Michael James a écrit :

 Angel,
 I've tested gripped JS for some other projects, and I know it works fine in 
 at least Firefox, Safari, Chrome, and Opera. Looks like all major browsers 
 are supported as of 2012.
 
 http://www.http-compression.com/#gzip
 
 Michael Evans
 Organic Chemistry Graduate Student, Moore Group
 University of Illinois, Urbana-Champaign
 
 On Nov 18, 2012, at 5:38 PM, Angel Herráez angel.herr...@uah.es wrote:
 
 Hi Paul
 
 I also tried Google Closure compiler a few days ago, but I was put off by 
 the 
 warnings, like this one:
 
 core.z.js:3435: WARNING - Suspicious code. This code lacks side-effects. Is 
 there a bug?
 ($t$ = java.net.URL.factory = fac, java.net.URL.prototype.factory = 
 java.net.URL.factory, $t$);
  
 ^
 
 
 Will gzipped JS files be accepted by all browsers?
 
 

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Re: [Jmol-users] JSmol advancements -- threads

2012-11-18 Thread Paul Pillot

Looks great !
Just for curiosity's sake, aren't web workers good alternative to threads in 
javascript ?

Le 19 nov. 2012 à 03:17, Robert Hanson a écrit :

 OK, we have basically everything we had in Jmol in terms of threads -- 
 tasks that run independently. It's a fake -- in a browser you get one thread. 
 Period. But I tried a simple setTimeout solution, and it worked perfectly. 
 
 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
 
 now has (in HTML5 mode, at least)
 
 animation
 delay
 hover
 moveto
 spin
 vibration
 
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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[Jmol-users] JSmol and Jquery mobile

2012-11-10 Thread Paul Pillot

This might be of interest to some of this list users,
I've tried to make a web app aimed at tablets or other mobile platforms using 
jsmol.
I tried the Jquery mobile framework to achieve this, but I had a very strange 
result regarding the Jmol canvas : rotation was unavailable (click and drag 
resulted only in scaling), and strangely the image definition was very poor (as 
if drawn in a very small size and rescaled to a bigger one).
Discarding the jquery mobile lib returned JSmol display back to normal.
I don't know where the bugs come from but the fact is that Jquery mobile 
framework is conflicting with Jsmol.
Paul
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Re: [Jmol-users] Give this a try...

2012-10-24 Thread Paul Pillot

This is fabulous !
I've just tried it on my laptop and on an Ipad, it worked great on both !
This unveils a new continent of possibilities, thank-you Bob ! 
Loading takes a bit of time for the first run : my browser pulled 313 requests. 
I suspect it could also be speed up by compressing the js files server-side and 
using caching in the browser for subsequent requests.
Paul

Le 24 oct. 2012 à 07:09, Robert Hanson a écrit :

 Totally HTML5 Jmol. I kid you not. You won't believe it's not Java. There is 
 no Java here. No WebGL. No hardware GPU acceleration. Just HTML5. Just Jmol 
 code.
 
 http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
 
 -- exact rendering duplication of Jmol
 -- full scripting
 -- all rendering options of Jmol including cartoons, surfaces, translucency, 
 balls, sticks, everything.
 
 TODO:
 
 -- no labels yet
 -- no binary file reading yet
 -- no picking, hover
 -- limited mouse action (rotate, zoom)
 -- file loading not optimized
 
 Bob
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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Re: [Jmol-users] Creating multiple instances of JmolViewer

2012-09-28 Thread Paul Pillot

There is just one Jmol object, but you can have several applets. Maybe what you 
describe is due to trying no create several Jmol objects ?
Paul

Le 28 sept. 2012 à 16:52, Andreas Truszkowski a écrit :

 Hi Bob,
 
 it seams that the first instance is updated by the executed scripts of the 
 second instance. E.g. lightning settings like  set zShadePower, set 
 ambientPercent,...
 
 Kind regards,
 Andreas
 
 Am 28.09.2012 16:31, schrieb Robert Hanson:
 
 
 On Fri, Sep 28, 2012 at 8:39 AM, Andreas Truszkowski atruszkow...@gmx.de 
 wrote:
 Hi,
 
 instanciating several JmolViewer instances leads in overwritin of each
 other. Am I right that Jmol is not thread safe?
 
 No. We do all sorts of things with multiple viewers. There are no static 
 objects, only static constants.
 
  
 What I am going to do:
   I will use one instance of the JmolViewer for displaying structures
 whereby another instance shall render images in a background thread.
 The code forinstantiation is
 viewer = JmolViewer.allocateViewer((panel or null), new
 SmarterJmolAdapter(),
  null, null, null, null, null);
 
 Is it possible to get it work in a single virtual machine or have I to
 run a second JVM to get this work?
 
 
 just allocate another viewer, and you should be fine. What exact problems 
 are you seeing? 
 
 Bob Hanson
  
 Kind regards,
 Andreas
 
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 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
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Re: [Jmol-users] write command to server

2012-09-21 Thread Paul Pillot



 Alex beat me to it. Right. Sorry, it's not the WRITE command. It's this:
 
 Var x = load(http://xxx.xxx.xxx/servlet/?POST?_PNGJBIN_;)
 
 You  will get a return from your server, but in the process Jmol will send 
 the PNGJ file in the  POST. I can send you the PHP side of this if you want 
 to see it. 
 
 Bob
 
It would be very valuable for me to have a look at the PHP code. I've made 
several trials some time ago, but could not find where the data is in $_POST 
Paul

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Re: [Jmol-users] Notify user if signed applet request is declined

2012-06-28 Thread Paul Pillot

Try jmolScriptWait() instead
Paul


Le 28 juin 2012 à 09:40, Martin Hediger a écrit :

 I tried show _signedApplet in the Jmol console, which nicely prints 
 true.
 However, jmolScript('show _signedApplet') on the console of the 
 browser returns undefined.
 
 
 
 
 
 
 
 
 On 27.06.12 15:19, Rolf Huehne wrote:
 On 06/27/2012 03:11 PM, Angel Herráez wrote:
 better:
 
 http://chemapps.stolaf.edu/jmol/docs/
 Read-Only Variables
 _signedApplet   
   whether or not Jmol is running as an signed applet (Jmol 11.6)
 
 This won't help in this case because the signed applet is running. But
 because the user denied the extra rights the browser is running it with
 the rights for the unsigned applet.
 
 Regards,
 Rolf
 
 
 
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Re: [Jmol-users] Resolver Test Request

2012-06-28 Thread Paul Pillot

Tried it twice today (morning and afternoon):
- first link has always worked
- second link never worked on the first attempt, only on the second try

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Re: [Jmol-users] Resolver Test Request

2012-06-28 Thread Paul Pillot

Otis,
you can use jQuery's ajax method to send a cross-domain request directly to the 
Resolver. You don't need to use jmolScript for that.
I think the only concern is that the browser has to accept XmlhttpRequest v2, 
which might be a problem with some version (all ?) of MIE.

I have a website that hits resolver too through php 
(http://librairiedemolecules.education.fr/outils/scribmol/scrib.html bottom 
text box Rechercher). It doesn't shows the same problem.

Paul

Le 28 juin 2012 à 15:49, Otis Rothenberger a écrit :

 Paul,
 
 That's an important piece of information.
 
 Markus, the problem could be in my server script. That does not explain why 
 I'm seeing a problem with the direct hit to Resolver on my end. Also, 
 remember that my initial success on link 1 (directly to Resolver) after 
 several tries, clears the way for link 2 in a separate browser tab.
 
 There might be another thing that I should explore. Bob mentioned something a 
 while back about the ability to make a direct hit from the virtual model kit 
 to Resolver. Is this possible? As it is now, I am using a JmolScript to load 
 your file via AJAX from my server. Did I understand Bob correctly? Is it 
 theoretically possible to hit Resolver directly via the JmolScript?
 
 Otis
 
 --
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 o...@chemagic.com
 http://chemagic.com
 
 
 
 
 On Jun 28, 2012, at 9:07 AM, Paul Pillot wrote:
 
 Tried it twice today (morning and afternoon):
 - first link has always worked
 - second link never worked on the first attempt, only on the second try
 
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Re: [Jmol-users] Notify user if signed applet request is declined

2012-06-27 Thread Paul Pillot

With getproperty appletInfo, you can access the name of the applet :
appletInfo.htmlName=jmolApplet0
From there, you can guess if it's signed or not... (haven't tried it but I 
suspect it should work)
Paul

Le 27 juin 2012 à 14:25, Martin Hediger a écrit :

 Just to be clear, I'm not reporting any error or bug here. I want to 
 implement a feature but I need to figure out the relevant part of the 
 Jmol API.
 I'll be checking the doc.
 
 
 
 
 
 On 27.06.12 13:26, Angel Herráez wrote:
 Martin, I agree with that observation.
 My feeling is that the unsigned applet is what gets loaded.
 
 1. Is the Jmol frank red or white?
 2. I think there is a Jmol read-only variable that will say if it is
 signed. Check the doc
 
 
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Re: [Jmol-users] Notify user if signed applet request is declined

2012-06-27 Thread Paul Pillot

Sorry, this doesn't work: the signed applet gives back the same name as the 
unsigned...
Last thing I can think of is a try{} catch {} where you could try to load a 
dummy file from a different domain...
Paul

Le 27 juin 2012 à 14:47, Paul Pillot a écrit :

 With getproperty appletInfo, you can access the name of the applet :
 appletInfo.htmlName=jmolApplet0
 From there, you can guess if it's signed or not... (haven't tried it but I 
 suspect it should work)
 Paul
 
 Le 27 juin 2012 à 14:25, Martin Hediger a écrit :
 
 Just to be clear, I'm not reporting any error or bug here. I want to 
 implement a feature but I need to figure out the relevant part of the 
 Jmol API.
 I'll be checking the doc.
 
 
 
 
 
 On 27.06.12 13:26, Angel Herráez wrote:
 Martin, I agree with that observation.
 My feeling is that the unsigned applet is what gets loaded.
 
 1. Is the Jmol frank red or white?
 2. I think there is a Jmol read-only variable that will say if it is
 signed. Check the doc
 
 
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Re: [Jmol-users] Question Jmol / CGI response

2012-06-21 Thread Paul Pillot

That's probably not related to the issue you reported, but this part of the js
might have performance issues : 
function build_interface(resp)
{
/* 
   Handling of Q_tot coming from bio_rho.cgi.
   Json does not work right now, probably problem on
   CGI side:
   var q_tot = jQuery.parseJSON(resp);
*/ 

// Q_tot evaluation.
var q_tot = resp.split(';')[0].split('=')[1];
$('#pHLab').html(Qsubtot/subat pH  + pH + :  + q_tot);

// Charge distribution evaluation.
var pqr = resp.split(';')[1].split('=')[1];
$('#pqr').attr(value, pqr); 

// Charge distribution.
jmolScript('load pqr::' + pdb_base_path + 
'%s-reo.pqr'.replace('%s', target+'-'+pHPad.split('\n')[0]));
jmolScript('select 1.1');
jmolScript('set propertycolorscheme rwb');
jmolScript('color property partialcharge'); 
jmolScript('spacefill 100%');
// Protein representation.
jmolScript('load APPEND ' + pdb_base_path + 
'%s-reo.pdb'.replace('%s', target));
jmolScript('select 2.1');
jmolScript('ribbons only');
// NW representation.
jmolScript('load APPEND ' + pdb_base_path + 
'nw_%s.xyz'.replace('%s', target));
jmolScript('select 3.1');
jmolScript('spacefill 20%');
// Display configuration. 
jmolScript('select 1.1 or 2.1');
jmolScript('set allowRotateSelected');
jmolScript('set dragSelected');
jmolScript('frame *');
// Report Jmol setup finished.
cr();
}
You should reduce the successive jmolScript calls to a single one, with 
distinct commands separated by semi-colons.
jmolScript function does many things before actually sending the script to the 
applet. The applet is more efficient at dealing
with a script.
Paul

Le 21 juin 2012 à 20:32, Martin Hediger a écrit :

 Dear Jmol Developers
 The next version of our application is almost ready.
 http://www.biofetsim.org/ku_prototype.html
 
 All features we want are in place, now we're basically debugging it and 
 cleaning it up.
 One bug which is difficult for me to track down is the following: you'll 
 notice a pH Response button on the page, which calls a server-side 
 application to compute a pH dependent signal of a protein on a 
 biosensor. This is dependent on the orientation of the biomolecule in 
 the Jmol applet. However, after rotating the molecule, the plot is only 
 updated once I click pH Response twice. What could be the problem?
 Our code base is hosted on Github, find our repository here:
 https://github.com/mzhKU/BioFET-SIM-WEB
 
 Any feedback for the above problem is highly welcomed. I'm happy to 
 provide also more details on the technical background of how the whole 
 site is setup.
 
 Best regards
 Martin
 
 
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Re: [Jmol-users] renaming Object Jmol files

2012-06-14 Thread Paul Pillot

Good idea !
Shall we bundle them in a single mimized js file ?
Paul

Le 12 juin 2012 à 20:49, Robert Hanson a écrit :

 I think I need to rename these so that they appear together and also are easy 
 to copy from one place to another:
 
 JmolCore.js  -- Jmol_Core.js
 JmolApplet.js-- Jmol_Applet.js
 JmolControls.js -- Jmol_Controls.js
 JmolApi.js  -- Jmol_Api.js
 JmolJSV.js -- Jmol_JSV.js
 JmolCD.js-- Jmol_CD.js
 JmolGLmol.js-- Jmol_GLmol.js
 
 what else?
 
 mousewheel.js -- Jmol_mousewheel.js
 gl-matrix-min.js  -- Jmol_gl-matrix-min.js
 Three49custom.js -- Jmol_Three49custom.js
 
 Objections? Comments? Suggestions?
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
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 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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Re: [Jmol-users] renaming Object Jmol files

2012-06-14 Thread Paul Pillot

Jmol_Lib.min.js ?
Jmol_Main.min.js ?
Jmol_All.min.js ?

Le 15 juin 2012 à 03:10, Robert Hanson a écrit :

 Jmol_App.js
 
 ?
 
 On Thu, Jun 14, 2012 at 7:25 PM, Robert Hanson hans...@stolaf.edu wrote:
 Bundling is a possibility. We need 
 
 JmolCore.js
 JmolApplet.js
 JmolApi.js
 
 JmolControls.js is optional, but it's pretty tiny. And they JmolCD.js, 
 JmolGLmol.js, JmolJME.js, JmolJSV.js are all independent and optional, so it 
 doesn't seem smart to bundle those. 
 
 For me it has been nice to have these as separate files, but maybe now it is 
 time to put the four main libraries. 
 
 JmolCore.js
 JmolApplet.js
 JmolApi.js
 JmolControls.js
 
 So then what do we call that? 
 
 Jmol_???.js
 
 I'd still like to add _ in the others so that one can do this:
 
 copy Jmol_*.js ...
 
 and they will all be together in my directories. 
 
 Bob
 
 
 
 
 On Thu, Jun 14, 2012 at 4:36 PM, Michael Evans evan...@illinois.edu wrote:
 A good idea from the standpoint of loading speed.
 
 Cheers, Mike
 
 ---
 Mike Evans
 Organic Chemistry Graduate Student, Moore Group
 University of Illinois, Urbana-Champaign
 
 
 
 On Thu, Jun 14, 2012 at 4:30 PM, Paul Pillot 
 paul.pil...@ac-orleans-tours.fr wrote:
 Good idea !
 Shall we bundle them in a single mimized js file ?
 Paul
 
 Le 12 juin 2012 à 20:49, Robert Hanson a écrit :
 
 I think I need to rename these so that they appear together and also are 
 easy to copy from one place to another:
 
 JmolCore.js  -- Jmol_Core.js
 JmolApplet.js-- Jmol_Applet.js
 JmolControls.js -- Jmol_Controls.js
 JmolApi.js  -- Jmol_Api.js
 JmolJSV.js -- Jmol_JSV.js
 JmolCD.js-- Jmol_CD.js
 JmolGLmol.js-- Jmol_GLmol.js
 
 what else?
 
 mousewheel.js -- Jmol_mousewheel.js
 gl-matrix-min.js  -- Jmol_gl-matrix-min.js
 Three49custom.js -- Jmol_Three49custom.js
 
 Objections? Comments? Suggestions?
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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 -- 
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 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
 
 
 
 -- 
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr
 
 
 If nature does not answer first what we want,
 it is better to take what answer we get. 
 
 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
 
 
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Re: [Jmol-users] Jmol/HTML5/WebGL

2012-06-11 Thread Paul Pillot

Might be relevant to this discussion,
I'm setting up a script to replace a Jmol png image (with state included) by an 
applet when user hovers the image and click on a link then displayed.
The first attempt can be seen there :
http://librairiedemolecules.education.fr/molecule.php?idmol=336
Try hovering any of the two images displayed and click on the link displayed at 
the bottom. If everything works, the image should be replaced by an applet 
executing the state script of the image (the image is send as a script to the 
applet).
I don't know if it works with IE, but it should work fine with other browsers...

Paul

Le 9 juin 2012 à 17:37, Rzepa Henry a écrit :

 
 On 9 Jun 2012, at 16:03, Robert Hanson wrote:
 
 I'm wondering what additional JavaScript-based 3D molecular visualization
 libraries people are interested in linking Jmol to. These could be
 HTML5-only, WebGL-only, or some combination. It might not be terribly
 difficult to implement that.
 
 Interest? Ideas?
 
 
 I have been asked by a publisher with whom  I am discussing replacing static 
 images with  HTML5/WebGL instances, to ensure that the minimal behaviour 
 always defaults to the replaced image (= the  Acrobat version of an article). 
   I wonder if it might be possible to define an array of such images (say 
 Figures 1-10)  which the  Jmol scripts can cascade down to if for whatever 
 reason the active scripts are not possible.
 
 I know that a  JPG can be generated server side to insert such an image, but  
 a pre-generated array of images would  be useful if the server-side 
 generation were not to be available (ie the same images that have been used 
 in the static  Acrobat version). 
 

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Re: [Jmol-users] Jmol/HTML5/WebGL

2012-06-11 Thread Paul Pillot

Thanks Angel !
(I don't know why messages didn't go to the list yesterday)
I've tried it at my school today with their IE8 and discovered exactly the same 
behavior as you described.
But I've tried it with other images such as the ones on this page 
http://librairiedemolecules.education.fr/molecule.php?idmol=304 (only n°2, 4 
and 5 are proper Jmol png) and could see that the png images were displayed.
So I am wondering if something wasn't broken in the latest Jmol version I used 
for creating the png images, at least with IE8 png interpreter. Those are not 
pngj files, but png files embedding the state script.

 
Le 11 juin 2012 à 19:23, Angel Herráez a écrit :

 Hi Paul 
 
 http://librairiedemolecules.education.fr/molecule.php?idmol=336
 
 Very nice!
 
 It works in my Firfox 13 / WinXP but IE8 does not even display the 
 images (why is it so?)
 
 On IE8, if I am quick to catch the link (which is located to the 
 bottom-right of the image space) and click on it, the Jmol applet 
 displays fine.
 
 
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Re: [Jmol-users] Jmol/HTML5/WebGL

2012-06-11 Thread Paul Pillot


Le 11 juin 2012 à 21:10, Angel Herráez a écrit :

 Testing in IE9 (64-bit, Win7):
 
 The IE console reports a javascript error at line 31,
 jmol = Jmol.getApplet( jmol, Info)
that's because is should be : jmol = Jmol.getApplet( jmol, Info)
(without quotes)

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Re: [Jmol-users] Eval Function

2012-05-17 Thread Paul Pillot

Have you tried this approach :
script APPLET appletName @{Jmol math expression}
(from the documentation)

Paul

Le 17 mai 2012 à 18:46, Otis Rothenberger a écrit :

 Bob,
 
 Is there a way to execute JmolScript that is in a string variable - i.e. an 
 eval function approach?
 
 Otis
 
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Re: [Jmol-users] Eval Function

2012-05-17 Thread Paul Pillot

Too quick ! The following is even better for your purpose :
script INLINE @{Jmol math expression}
Runs the script command result of the Jmol math expression rather than from a 
file. The math expression may be a simple single variable name or a more 
complex expression. For example, var bgColor=red;script INLINE @{background 
 + bgColor} or var s = [arg];script INLINE @{select  + s}.
Paul

Le 17 mai 2012 à 18:46, Otis Rothenberger a écrit :

 Bob,
 
 Is there a way to execute JmolScript that is in a string variable - i.e. an 
 eval function approach?
 
 Otis
 
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Re: [Jmol-users] Jmol partial charge calculation

2012-05-12 Thread Paul Pillot

Otis,
I think the green surface is great and I was just wondering how it could be 
displayed for alkanes. My guess is that it's not displayed because when there 
is no partial charge, no MEP surface can be created. The problem is how does 
Jmol guess there is no partial charge in the file?, and the answer seems to be 
when all partial charges are set to 0.0. This rule appears to work generally 
except for alkanes, even if it can look silly to search for polarity on alkanes 
!
Paul

Le 11 mai 2012 à 18:13, Otis Rothenberger a écrit :

 Paul,
 
 I need to clean that up on my page by trapping the zero partial charge on 
 alkanes. I don't know much about the calculation that Bob installed, but the 
 PUBCHEM_MMFF94_PARTIAL_CHARGES for alkanes are also zero. I was trapping 
 those files and making a slight adjustment to at least show the green surface 
 that suggests close to non-polar bonding. I broke this trap when I was adding 
 the dynamic MEP feature. Thanks for picking up on this.
 
 Otis 
 
 
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 On May 11, 2012, at 10:47 AM, Pillot Paul wrote:
 
 I've played with this new feature as well and I've found an unexpected 
 behavior : when the molecule is an alkane the VDW surface is not computed 
 and an error is issued, stating that the file does not contain partial 
 charges to display the MEP surface.
 
 The calculate partialcharge command runs just fine. Of course there are no 
 partial charges for these alkane models so that is certainly the cause for 
 the error.
 
 
 
 Nonetheless, in modelkit, if I create first a model with partial charges 
 and a MEP surface, and I subsequently remove from that model atoms or 
 reduce bonds order to get an alkane, then a green MEP surface is displayed.
 
 
 
 In Otis' page, this problem doesn't appear when one chooses to start from 
 C2H6 (green MEP surface is displayed). I suspect that's because the 
 ethene.txt file used there has charges set (-0.0680 for C and 0.0227 for H) 
  ... In Bob's simple page, this can be tested by loading ethan from NCI 
 and try to display MEP (no surface displayed).
 
 Paul
 
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Re: [Jmol-users] Jmol partial charge calculation

2012-05-09 Thread Paul Pillot

I am not an expert here... Is there a significative change in computational 
time or in the results obtained from what can be done with the currently 
implemented UFF ?
Paul

Le 9 mai 2012 à 02:50, Robert Hanson a écrit :

 I guess the next step is to implement MMFF94 in Jmol.  I had been avoiding 
 that because of the difficulty in atom typing. But now that that's done, the 
 rest is reasonably straightforward. Still, it's quite a chore. I don't think 
 it will happen this week Would this be a valuable addition or going too 
 far into the calculation arena?
 
 Bob
 
 
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 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
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 it is better to take what answer we get. 
 
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Re: [Jmol-users] Jmol partial charge calculation

2012-05-08 Thread Paul Pillot

This is brilliant !
In case somebody is wondering how to display labels showing the partial charges 
:
label %[partialCharge]

Paul

Le 8 mai 2012 à 22:04, Robert Hanson a écrit :

 OK, this is working.
 
 http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm
 
 load a model by name from either PubChem or NCI
 
 then click on the button on the right that reads show/hide MEP
 
 
 Bob
 
 
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
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 it is better to take what answer we get. 
 
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

2012-04-21 Thread Paul Pillot

How does this work technically (JSONP ? other ?) ? I thought it was not 
possible to make ajax calls to other domains without triggering a security 
message (to prevent cross site scripting) ?
It's very exciting to see this working so well without the signed applet !
Paul

Le 21 avr. 2012 à 01:56, Robert Hanson a écrit :

 yes indeedy, both  NCI and PDB allow direct access via AJAX to their 
 databases. Thank you, guys!
 
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
 
 Thus, with Jmol/ChemDoodle there is no need to go to the server except for an 
 image.
 
 
 On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger osrot...@chemagic.com 
 wrote:
 
 

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Re: [Jmol-users] Jmol/ChemDoodle -- test2

2012-04-17 Thread Paul Pillot

Bob,
I am still working on a rewrite of Jmol.js
It takes time, but my efforts are going in the same way as the library you made.
Hope I could make it available soon.

Paul

Le 17 avr. 2012 à 14:11, Robert Hanson a écrit :

 
 
 2012/4/17 Angel Herráez angel.herr...@uah.es
  Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is
  a library of extensions to ChemDoodle. What it actually does is to
  create a high-level object called Jmol (conveniently!) that loads
  applets in a new way. I think it is our new Jmol object JavaScript.
  And I suggest we make it THE development platform for the applet.
 
 This sounds like an exciting advance, and I'm just so sorry that I
 cannot follow it more closely now.
 My suggestion is that this change in Jmol.js dealing with applet
 objects is quite radical, and maybe justifies a change in major
 version number. That is, close down 12.4 with the old method and
 start 12.5 when the new Jmol.js starts to be developed.
 That would help sort out problems by making more apparent to users
 that a new system has been adopted (even though the users might not
 really notice the change since all is run behind the curtains by
 Jmol.js)
 
 
 I think that's a great idea. Won't happen until June or July, but we can aim 
 for that. 
  
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Re: [Jmol-users] Jmol/ChemDoodle -- test1

2012-04-12 Thread Paul Pillot

How does this work ?
It apparently makes a call to a php script hosted on stolaf's server. Does this 
php script itself calls jmoldata.jar server side ?
And how does it replies ? by sending back a mol file or a chemdoodle JSON 
object ?
-Paul 
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