Re: [Jmol-developers] ADFReader AtomType

[Robert Hanson]

Jmol.___JmolVersion="14.20.1"

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


This reads N.test as symbol="N" and name="N.text"




On Mon, Jul 3, 2017 at 7:20 AM, Georg Eickerling <
georg.eickerl...@physik.uni-augsburg.de> wrote:

> Dear all,
>
> this is some kind of feature addon for the Jmol filters:
>
> The ADF filter obviously assumes all element symbols to be simple
> strings. This is not always true following the ADF user guide
>
> https://www.scm.com/doc.2016/ADF/Input/Atomic_coordinates.
> html?highlight=atoms
>
>  were "atom types" are
>
> ***
> AtomType
>
> The name of an atom type. It must begin with the standard one- or
> two-character symbol for the chemical element (e.g. H, He, Li,...).
> Optionally it may be appended by .text, where text is any string (not
> containing delimiters). Examples: H, Mn.3, Cu.dz-new.
> ***
>
> This feature is for example used in NMR coupling calculations when
> re-defining special basis sets for some of the coupling atoms.
>
> At the moment, the jmol parser apparently simply ignores atoms with
> names such as "H.b" so they are just lacking in the final structure. I
> suggest the following one line fix:
>
> ADFReader.java
>
> starting from line 159:
>
> while (rd() != null && !line.startsWith(" -")) {
>   tokens = getTokens();
>   if (tokens.length < 5)
> break;
>   String symbol = tokens[1];
>   /* +ADD THIS++ */
>   if(symbol.contains("."))
>   {
> symbol = symbol.split("\\.")[0];
>   }
>   /* +ADD THIS++ */
>   if (JmolAdapter.getElementNumber(symbol) < 1)
> nXX++;
>   else
> addAtomXYZSymName(tokens, pt0, symbol, null);
> }
>
> This will just split off the things after the period and proceed with
> the element symbol as usual and works for me on my local files with
> "H.b" atoms.
>
>
> best
>
> Georg
>
>
>
>
>
>
>
>
>
>
> --
> ~~~
>  PD Dr. Georg Eickerling
>  Universität Augsburg
>  Institut für Physik
>  Lehrstuhl für Chemische Physik und Materialwissenschaften
>  ~~~
>
> 
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it is better to take what answer we get.

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Re: [Jmol-developers] set antialiasdisplay needs a click to aply changes

[Robert Hanson]

good catch. Found and fixed. Behavior changed in 14.6.1 Aug 2016.

On Mon, Jun 19, 2017 at 2:34 PM, Angel Herráez  wrote:

> Dear Bob,
>
> We are finding a strange behaviour in JSmol-html5 within Proteopedia:
> changing antialiasDisplay does not display any effect until you click on
> the
> JSmol canvas.
>
> Test case: go to
> http://proteopedia.org/wiki/index.php/1a2m
> open the JSmol console and type
>
> zoom 300
> set antialiasDisplay true
> // no visible change until one clicks on JSmol
> set antialiasDisplay false
> // again
>
> Using "refresh" does not make any difference.
>
> And Eric just found that this problem is present in the Jmol application
> (from
> October 21, 2016)
> My copy, Jmol 14.10.0 2017-03-25, also does it:
> load =1a2m
> zoom 300
> cartoon only
> set antialiasDisplay true
>
> Another quirk: in that Proteopedia page, see how the font size of the echo
> text changes dramatically with antialias
>
>
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> 
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-developers] scripts persisting after quit or exit

[Robert Hanson]

On Mon, Apr 17, 2017 at 3:01 PM, Angel Herráez  wrote:

> Hi Jeff
>
> Glad you are finding a solution. The lack of working of "!exit" straight
> away is
> disturbing.
>

exit

to work the way you want must be the first command in a script. Otherwise
it just acts on the currently running script (it's script) and clears the
queue of all remaining unprocessed scripts.

Bob
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Re: [Jmol-developers] [Jmol-users] Jmol on Maven Central

[Robert Hanson]

Jmol.___JmolVersion="14.8.0"

Release Note: switching to semantic versioning (http://semver.org/)
Release Note: When releasing beta versions, add "-beta--MM-DD"

This change replaces the former nonstandard Jmol.major.minor.patch_.mm.dd
syntax where there were two running SVN directories, one for odd minor
version (trunk; beta) and one for even minor version  (branch v14_6,
release).

While this worked, it required unnecessary and nonstandard maintenance, and
it caused problems with Maven. Now the way it will work is that all
development, even bug fixes, will be on the trunk.


Bug fixes will be patch level x.x.X; new features mostly will be minor
level x.X.x. SVN updates and versions will be listed as "-beta" if there is
a concern that new features need testing, and without that for a full
release.

Releases will continue to be sent to https://sourceforge.net/
projects/jmol/files/Jmol-beta and https://sourceforge.net/
projects/jmol/files/Jmol depending upon the  -beta flag.

-beta releases will continue to be only be the binary.zip file. "Full"
releases, without the -beta flag, will include all three files (binary.zip,
binary.tar.gz, and full.tar.gz)

Only non-beta will be tagged for Maven. (Just did this now for 14.8.0)

Bob
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Re: [Jmol-developers] Fwd: [sage-cell] Re: Encoding problems for jsmol context menu

[Robert Hanson]

On Wed, Nov 9, 2016 at 3:13 AM, Angel Herráez  wrote:

> Hi Jonathan
>
> while https://sagecell.sagemath.org/embedded_sagecell.js seems to be
> encoded as "windows-1252"
>
>
that would do it.
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Re: [Jmol-developers] Is it possible to create a .dll?

[Robert Hanson]

No, it's not a Windows program. It's a Java program. Unity probably does
not work with Java.

On Tue, Oct 25, 2016 at 9:37 AM, Anastasya Karchevskaya 
wrote:

> Good day, everyone!
>
> I am trying to make an app with Unity (not UnityMol, different, but I need
> to visualise molecules as well). I have tried to use JS files like a
> library inside Unity but failed, probably because Unity tries to interpret
> them as unityScript and fails. But I had success with using OBBotNet.dll
> (form OpenBabel) inside my project for calculations and conversions. Now,
> is it possible to make a .dll from JMol/JSMol files and to add it to Unity?
>
> Thank you,
>
> Anastasia
> 
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-- 
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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
--
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Re: [Jmol-developers] export to IDTF is brokwn

[Robert Hanson]

I remember the problem now. It is that there is no default view, so it is
absolutely necessary to add the additional features that create the view in
the PDF file separately, as illustrated in the LaTex that Jmol produces.

http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-363%204th%20Edition.pdf

*8.3 There is no default model node, default light node, nor default view
node.*


On Wed, Oct 19, 2016 at 3:18 AM, Angel Herráez <angel.herr...@uah.es> wrote:

> El 18 Oct 2016 a las 23:06, Robert Hanson escribió:
> > IDTF does work correctly now, but you have to use the additional LaTex
> file generated by Jmol to
>
> Yes, I had seen that part. However, I was expecting for a way to make a
> complex PDF (with text, flow, etc) without learning Latex. The PDF
> generated with Jmol's two files just holds the 3D model.
> My idea was to design my layout e.g. in Word, leaving empty squares for the
> models, produce the PDF, then edit it with PowerPDF and insert the u3d
> files. It works except the model is often either out of view or terribly
> zoomed
> in. Will keep trying.
>
> > orient it, because that is where the orientation information is. (IDTF
> was designed specifically to
> > not allow specifying of orientation. Go figure!)
>
> Wow!
>
>
> Thank you
>
>
> 
> --
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-- 
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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
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Re: [Jmol-developers] export to IDTF is brokwn

[Robert Hanson]

IDTF does work correctly now, but you have to use the additional LaTex file
generated by Jmol to orient it, because that is where the orientation
information is. (IDTF was designed specifically to *not* allow specifying
of orientation. Go figure!)

Bob


On Tue, Oct 18, 2016 at 3:43 AM, Angel Herráez  wrote:

> > thank you. fixed. Are people still using IDTF?
>
> Yes, hardly anyone, given the amount of information that can be found
> online. Still, there is some life -- see [1]
> But I am picking again the idea of producing PDFs with 3D models, and IDTF
> -> U3D is the only route.
> I just found that Power PDF fron Nuance lets you insert a u3d file in a
> PDF, together with all the other content, very easily and visually within
> the GUI. So I am giving it a try. Seems t work very nicely except for wrong
> zoom / position of the model.
> With a price of 39€ for the Education version of the software, it's worth
> the effort. Much nicer than learning Latex.
>
> [1]
> Embedding and publishing interactive, 3-dimensional, scientific figures in
> portable document format (PDF) files. Barnes, Vidiassov et al. (2013)
> doi:10.1371/journal.pone.0069446
>
>
>
>
> 
> --
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>


-- 
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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
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Re: [Jmol-developers] export to IDTF is brokwn

[Robert Hanson]

thank you. fixed. Are people still using IDTF?

On Mon, Oct 17, 2016 at 2:44 PM, Angel Herráez  wrote:

> Dear Bob,
>
> load $aspartate;
> write IDTF Asp.idtf
>
> does nothing, reports nothing
>
> Jmol 14.6.4, 2016-10-02  application
>
>
> ---
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>
>
> 
> --
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>



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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-developers] (bug) set measurement in angstroms

[Robert Hanson]

I have added the fix for this to the version I hope to release tomorrow.

Jmol.___JmolVersion="14.7.4_2016.10.08"

bug fix: SET MEASUREMENTS x.x  is 10x too wide

bug fix: MO command does not allow SQUARED with PLANE
bug fix: MO command SQUARED does not reset cutoff to its square
bug fix: MO command does not preserve SQUARED after PLANE command

bug fix: MOLDEN reader does not accept [MOLDEN FORMAT]

bug fix: WRL/X3D/STL surface closure for rockets, cartoons, polyhedra,
ellipsoids, geosurface, draw
bug fix: triangle renderer miscalculates z-index, causing some hidden
triangle bits to show



On Sat, Oct 8, 2016 at 9:51 AM, Angel Herráez  wrote:

> set measurements 0.25
>
> (any width in angstroms)
> is failing in versions below -- it used to work as expected, giving a not
> s
> thick cylinder
>
> 14.6.4_2016.10.02
> 14.6.2_2016.08.28
> 14.7.0_2016.06.27
> 14.6.0_2016.06.22 used at Proteopedia
>
>
> ---
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>
> 
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-- 
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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
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Re: [Jmol-developers] cannot write menu to file in 14.6.2

[Robert Hanson]

fixed.

OK, the issue here was that the JavaScript function btoa(string) does not
work with UTF-8-encoded strings. The solution was to use
string.getBytes("UTF-8") to get a proper byte array, and then use Jmol's
own base64 encoder to turn that into base64.



On Sat, Sep 17, 2016 at 4:58 PM, Angel Herráez <angel.herr...@uah.es> wrote:

> Well, guess what
>
> It does not work for me in your page, but it does after I change the
> language to US English in the popup menu
>
> It only likes to save the English menu ;.)
>
> Forget it
>
> ----------
>
> On 17 Sep 2016 at 15:51, Robert Hanson wrote:
>
> write menu ?
>
> worked fine for me at *https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm*
> <https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm>
>
>
>
> On Sat, Sep 17, 2016 at 10:29 AM, Angel Herráez < *angel.herr...@uah.es*
> <angel.herr...@uah.es>> wrote:
> Ok, thanks
>
> I have later been able to do it from Java applet - so it may be that
>
> --
>
> On 17 Sep 2016 at 9:53, Robert Hanson wrote:
>
> I don't think write menu was implemented in JSmol. Will take a look.
>
>
> 
> --
>
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>
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> 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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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-developers] cannot write menu to file in 14.6.2

[Robert Hanson]

write menu  ?

worked fine for me at https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm



On Sat, Sep 17, 2016 at 10:29 AM, Angel Herráez <angel.herr...@uah.es>
wrote:

> Ok, thanks
>
>  I have later been able to do it from Java applet - so it may be that
>
> --
>
> On 17 Sep 2016 at 9:53, Robert Hanson wrote:
>
> I don't think write menu was implemented in JSmol. Will take a look.
>
>
>
> 
> --
>
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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-developers] cannot write menu to file in 14.6.2

[Robert Hanson]

I don't think write menu was implemented in JSmol. Will take a look.

On Sat, Sep 17, 2016 at 5:37 AM, Angel Herráez  wrote:

> Is this a bug?
>
> On https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>
> in the console:   " write menu ? "
> gives this error after requesting the file name:
>
> ERROR en guión: TypeError: er.printStackTrace is not a function
>
>
> 
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-- 
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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
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

something like:

$("ul.jmolPopupMenu ul:not(:has(ul))").css({"maxHeight":"25em",
"overflowY":"auto"})

But I don't think that is quite it.

On Fri, Sep 16, 2016 at 1:16 PM, Angel Herráez  wrote:

> I like CSS solutions; they are very clean and you do not mess up with the
> js code.
>
> > something like "menus that do not contain any menus" --- li with no
> containing ul --- I think that can be done in jQuery. Can it be done in CSS?
>
> Not actually straightforward, since you cannot apply css to parent nodes
> based on their children; the logic it's the other way around, top-down.
> So I don't see how jQuery would do it -- it would have to resort to
> checking all ul and li elements using JS before deciding.
>
> Anyway, why target terminal submenus? It's their height that brings
> trouble, not their level in hierarchy.
>
>
>
>
>
>
> 
> --
>
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-- 
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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
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

something like "menus that do not contain any menus" --- li with no
containing ul --- I think that can be done in jQuery. Can it be done in
CSS?

On Fri, Sep 16, 2016 at 12:40 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> We might be able to implement that only for terminal menus. Have to think
> about how to do that.
>
> On Fri, Sep 16, 2016 at 12:39 PM, Robert Hanson <hans...@stolaf.edu>
> wrote:
>
>> I registered 2700 MSIE uses in April; 1.4% of 189,000.
>>
>> On Fri, Sep 16, 2016 at 12:41 PM, Angel Herráez <angel.herr...@uah.es>
>> wrote:
>>
>>> > The way too long problem is generally solved by dragging the menu
>>> higher
>>> on the screen.
>>>
>>> I know. But still sometimes it's higher than the screen.
>>> In many pages of mine the JSmol panel is 100% height, locked and cannot
>>> be scrolled down (overflow:none), so it's actually impossible to reach the
>>> lower submenus. That's how I noticed.
>>> Example: http://biomodel.uah.es/en/model1/prot/alfa.htm
>>>
>>>
>>> > It's a standard jQuery menu.
>>> > So if you can figure out
>>> > how to solve this with that, we could implement your solution in
>>> JSmol.
>>>
>>> Indeed. But  I found a trick using just css.
>>> See demo at
>>> http://biomodel.uah.es/model1j/prot/alfa.htm
>>> which is using a css patch in the page over regular JSmol.
>>> The code is
>>> .jmolPopupMenu ul.ui-menu { max-height:25em; overflow-y:auto;
>>> overflow-x:hidden; position:fixed; }
>>>
>>> That makes scrollable just the Language submenu and those like
>>> Select > Protein > by residue name
>>>
>>> However this patch breaks the unfolding of sub-submenus in IE11 (how
>>> much we should care about
>>> that browser, I'm not sure)
>>> There is a trick also to avoid applying the former rules for IE11,
>>> though it uses
>>> a dirty hack:
>>> @media screen and (min-width:0\0) {
>>> .jmolPopupMenu ul.ui-menu { max-height:none; overflow:hidden;
>>> position:absolute; }
>>> }
>>>
>>>
>>> Additionally, maybe personal taste, so I will not push for these to be
>>> implemented:
>>>  to reduce the height of each submenu element:
>>>
>>> ul.jmolPopupMenu , ul.jmolPopupMenu ul { line-height:1em; }
>>> /* or maybe 1.1em */
>>>
>>> and to reduce the size of the checkboxes and so the height of their
>>> submenu items (like langs):
>>>
>>> .jmolPopupMenu input[type="checkbox"] { transform: scale(0.8);
>>> margin-top:-0.2em; }
>>>
>>>
>>>
>>> 
>>> --
>>>
>>> ___
>>> Jmol-developers mailing list
>>> Jmol-developers@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

We might be able to implement that only for terminal menus. Have to think
about how to do that.

On Fri, Sep 16, 2016 at 12:39 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> I registered 2700 MSIE uses in April; 1.4% of 189,000.
>
> On Fri, Sep 16, 2016 at 12:41 PM, Angel Herráez <angel.herr...@uah.es>
> wrote:
>
>> > The way too long problem is generally solved by dragging the menu higher
>> on the screen.
>>
>> I know. But still sometimes it's higher than the screen.
>> In many pages of mine the JSmol panel is 100% height, locked and cannot
>> be scrolled down (overflow:none), so it's actually impossible to reach the
>> lower submenus. That's how I noticed.
>> Example: http://biomodel.uah.es/en/model1/prot/alfa.htm
>>
>>
>> > It's a standard jQuery menu.
>> > So if you can figure out
>> > how to solve this with that, we could implement your solution in
>> JSmol.
>>
>> Indeed. But  I found a trick using just css.
>> See demo at
>> http://biomodel.uah.es/model1j/prot/alfa.htm
>> which is using a css patch in the page over regular JSmol.
>> The code is
>> .jmolPopupMenu ul.ui-menu { max-height:25em; overflow-y:auto;
>> overflow-x:hidden; position:fixed; }
>>
>> That makes scrollable just the Language submenu and those like
>> Select > Protein > by residue name
>>
>> However this patch breaks the unfolding of sub-submenus in IE11 (how much
>> we should care about
>> that browser, I'm not sure)
>> There is a trick also to avoid applying the former rules for IE11, though
>> it uses
>> a dirty hack:
>> @media screen and (min-width:0\0) {
>> .jmolPopupMenu ul.ui-menu { max-height:none; overflow:hidden;
>> position:absolute; }
>> }
>>
>>
>> Additionally, maybe personal taste, so I will not push for these to be
>> implemented:
>>  to reduce the height of each submenu element:
>>
>> ul.jmolPopupMenu , ul.jmolPopupMenu ul { line-height:1em; }
>> /* or maybe 1.1em */
>>
>> and to reduce the size of the checkboxes and so the height of their
>> submenu items (like langs):
>>
>> .jmolPopupMenu input[type="checkbox"] { transform: scale(0.8);
>> margin-top:-0.2em; }
>>
>>
>>
>> 
>> --
>>
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

I registered 2700 MSIE uses in April; 1.4% of 189,000.

On Fri, Sep 16, 2016 at 12:41 PM, Angel Herráez 
wrote:

> > The way too long problem is generally solved by dragging the menu higher
> on the screen.
>
> I know. But still sometimes it's higher than the screen.
> In many pages of mine the JSmol panel is 100% height, locked and cannot be
> scrolled down (overflow:none), so it's actually impossible to reach the
> lower submenus. That's how I noticed.
> Example: http://biomodel.uah.es/en/model1/prot/alfa.htm
>
>
> > It's a standard jQuery menu.
> > So if you can figure out
> > how to solve this with that, we could implement your solution in
> JSmol.
>
> Indeed. But  I found a trick using just css.
> See demo at
> http://biomodel.uah.es/model1j/prot/alfa.htm
> which is using a css patch in the page over regular JSmol.
> The code is
> .jmolPopupMenu ul.ui-menu { max-height:25em; overflow-y:auto;
> overflow-x:hidden; position:fixed; }
>
> That makes scrollable just the Language submenu and those like
> Select > Protein > by residue name
>
> However this patch breaks the unfolding of sub-submenus in IE11 (how much
> we should care about
> that browser, I'm not sure)
> There is a trick also to avoid applying the former rules for IE11, though
> it uses
> a dirty hack:
> @media screen and (min-width:0\0) {
> .jmolPopupMenu ul.ui-menu { max-height:none; overflow:hidden;
> position:absolute; }
> }
>
>
> Additionally, maybe personal taste, so I will not push for these to be
> implemented:
>  to reduce the height of each submenu element:
>
> ul.jmolPopupMenu , ul.jmolPopupMenu ul { line-height:1em; }
> /* or maybe 1.1em */
>
> and to reduce the size of the checkboxes and so the height of their
> submenu items (like langs):
>
> .jmolPopupMenu input[type="checkbox"] { transform: scale(0.8);
> margin-top:-0.2em; }
>
>
>
> 
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

That's right, because the menu is based on an array in Language.js, not
from a po file, like the word "Russian" is. Language is one of the classes
that is included in corejmol.z.js. (If it were any other way, it would
require loading all the language files initially.)

Anyway, that is fixed.


On Fri, Sep 16, 2016 at 10:21 AM, Angel Herráez 
wrote:

> Fine, Bob
>
> The funny thing was that the first string (language name translated to
> current
> name) was correct, the second was wrong (language name in the original
> language).  If you siwtch to Russian, you can see in the same line one
> correct, one wrong.
>
> So I understand this is fixed for next release. Great!
>
> Regarding the height of the submenu, I think I have a solution via css (see
> http://biomodel.uah.es/Jmol/test/menu.htm bottom image)
> but where is the source for that part that generates the popup in JSmol?
>
>
>
>
>
> 
> --
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>



-- 
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-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

The way too long problem is generally solved by dragging the menu higher on
the screen. I'm not sure there is any other solution than that. It's a
standard jQuery menu. So if you can figure out how to solve this with that,
we could implement your solution in JSmol.

On Thu, Sep 15, 2016 at 3:29 AM, Angel Herráez  wrote:

> Dear Bob,
>
> I have noticed two issues with the rendering of the pop-up menu in
> JSmol-html5
>
> 1. The language submenu is way too long, and may become taller than the
> screen, so in some page designs the lower half of the languages may be
> unreachable.
>
> 2. The names of some languages display wrong characters (replaced by
> symbols by the browser)
>
> I would like to try and improve these, but I am having trouble locating
> the relevant source code where the rendering of the menu is generated. Can
> you give me a pointer?
>
> Thanks
>
> [image: graphic]
>
> 
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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


hts_1.PNG
Description: Binary data
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

Better -- I was missing the --charset UTF-8 flag on the Google Closure
Compiler command line.

On Fri, Sep 16, 2016 at 10:00 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> Hmm. This will be a good challenge.
>
> 1) The .java files are OK -- For example, Catal[`a] is correctly C3A0.
> 2) The .js files are fine.
> 3) In the developer console, everything is OK:
>
> x = "Català"
> "Català"
> x
> "Català"
>
> 4) The JavaScript is messed up:
>
> x = J.i18n.Language.getLanguageList()[4].nativeLanguage
> "Catal+�"
>
>
> 5) When I replace j2s/core/corejmol.z.js with  corejmol.js, it works.
>
> x = J.i18n.Language.getLanguageList()[4].nativeLanguage
> "Català"
>
> Hooray! The Google Closure Compiler is messing up.
>
> So you can do that yourself. This explains why it is only in the menu. I
> will remove Language.js from that compression, and we should be good to go.
>
> Bob
>
>
>
> On Thu, Sep 15, 2016 at 3:29 AM, Angel Herráez <angel.herr...@uah.es>
> wrote:
>
>> Dear Bob,
>>
>> I have noticed two issues with the rendering of the pop-up menu in
>> JSmol-html5
>>
>> 1. The language submenu is way too long, and may become taller than the
>> screen, so in some page designs the lower half of the languages may be
>> unreachable.
>>
>> 2. The names of some languages display wrong characters (replaced by
>> symbols by the browser)
>>
>> I would like to try and improve these, but I am having trouble locating
>> the relevant source code where the rendering of the menu is generated. Can
>> you give me a pointer?
>>
>> Thanks
>>
>> [image: graphic]
>>
>> 
>> --
>>
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


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


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

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


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Description: Binary data
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu

[Robert Hanson]

Hmm. This will be a good challenge.

1) The .java files are OK -- For example, Catal[`a] is correctly C3A0.
2) The .js files are fine.
3) In the developer console, everything is OK:

x = "Català"
"Català"
x
"Català"

4) The JavaScript is messed up:

x = J.i18n.Language.getLanguageList()[4].nativeLanguage
"Catal+�"


5) When I replace j2s/core/corejmol.z.js with  corejmol.js, it works.

x = J.i18n.Language.getLanguageList()[4].nativeLanguage
"Català"

Hooray! The Google Closure Compiler is messing up.

So you can do that yourself. This explains why it is only in the menu. I
will remove Language.js from that compression, and we should be good to go.

Bob



On Thu, Sep 15, 2016 at 3:29 AM, Angel Herráez  wrote:

> Dear Bob,
>
> I have noticed two issues with the rendering of the pop-up menu in
> JSmol-html5
>
> 1. The language submenu is way too long, and may become taller than the
> screen, so in some page designs the lower half of the languages may be
> unreachable.
>
> 2. The names of some languages display wrong characters (replaced by
> symbols by the browser)
>
> I would like to try and improve these, but I am having trouble locating
> the relevant source code where the rendering of the menu is generated. Can
> you give me a pointer?
>
> Thanks
>
> [image: graphic]
>
> 
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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-developers] "color darkgrey" is rejected

[Robert Hanson]

of course, we could just not use "darkgrey"

On Fri, Sep 2, 2016 at 2:08 PM, Angel Herráez  wrote:

> Bob,
> I know you worked on this recently.
> I am testing this on "14.6.2_2016.08.28  2016-08-28 07:48"
>
> color gray
> color grey
> color lightgray
> color lightgrey
> color darkgray // all ok up to here
> color darkgrey // script ERROR: a color or palette name (Jmol, Rasmol) is
> required
>
>
>
> 
> --
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>



-- 
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-developers] Tag Jmol releases

[Robert Hanson]

All my release notes are in
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Can I just add some information that works for you there?


On Wed, Aug 31, 2016 at 4:01 AM, Spencer Bliven <spencer.bli...@gmail.com>
wrote:

> We should definitely find a solution that doesn't increase the work for
> making a release. One solution that might be easier to automate than SVN
> tags is to include the SVN revision in README-xxx.properties. Then I could
> be sure that I'm checking out the correct revision without adding any more
> steps to the release procedure. I'll look into additional options for
> automating that with ant.
>
> On Tue, Aug 30, 2016 at 8:56 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> The date stamp on the file name is important and effectively constitutes
>> the minor version. Jar files are only updated at SVN on release (as part of
>> tar or zip files). You  should only be updating releases. I don't think it
>> will be manageable on my end to create new subminor versions 0.0.n  for
>> every check-in. But one thing I could do is release the first dated version
>> without a date if that helps. Just [14.6.3]. Would that somehow help? I'd
>> rather not do that, though.
>>
>> On Tue, Aug 30, 2016 at 3:16 AM, Spencer Bliven <spencer.bli...@gmail.com
>> > wrote:
>>
>>> I would advocate that maven should get a new artifact whenever
>>> sourceforge gets a new jar. For this reason I've been including the date as
>>> part of the version number. There is no way to silently replace a previous
>>> jar without giving it a new version number, so we can't just have a
>>> "14.6.2" branch that will get updated every week.
>>>
>>> I would just do a svn copy every time you push something to sourceforge.
>>> Probably there is a way to automate this in ant, but I'd have to look into
>>> it. Manually, something like
>>>
>>> svn copy http://svn.code.sf.net/p/jmol/code/branches/v14_6
>>> http://svn.code.sf.net/p/jmol/code/tags/v14_6_2_2016_08_28
>>>
>>> BTW, I'll be at the Web-based molecular graphics conference next week,
>>> so we can discuss details then if you want.
>>>
>>> -Spencer
>>>
>>> On Mon, Aug 29, 2016 at 7:45 PM, Robert Hanson <hans...@stolaf.edu>
>>> wrote:
>>>
>>>> I would not expect any Maven updates until there is an actual release,
>>>> as I did yesterday. What you are seeing there are minor bug fixes. If I can
>>>> tag those in some way, I'd be happy to do that.
>>>>
>>>> On Mon, Aug 29, 2016 at 7:42 AM, Spencer Bliven <
>>>> spencer.bli...@gmail.com> wrote:
>>>>
>>>>> Would it be possible to start creating tags for all releases? I think
>>>>> the last couple maven releases might have included a few commits more than
>>>>> they should have because I just used the head of the 14_6 branch. For
>>>>> instance, the "14.6.2_2016.08.28" on maven central was built from r21231.
>>>>> I'm not certain whether this matches the revision on sourceforge or 
>>>>> whether
>>>>> one of the other five commits on 8-28-2016 would have been better. This
>>>>> would be much easier to track if the process of releasing to sourceforge
>>>>> included a tagging step.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Spencer
>>>>>
>>>>> 
>>>>> --
>>>>>
>>>>> ___
>>>>> Jmol-developers mailing list
>>>>> Jmol-developers@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>>
>>>> 
>>>> --
>>>>
>>>> 

Re: [Jmol-developers] Tag Jmol releases

[Robert Hanson]

The date stamp on the file name is important and effectively constitutes
the minor version. Jar files are only updated at SVN on release (as part of
tar or zip files). You  should only be updating releases. I don't think it
will be manageable on my end to create new subminor versions 0.0.n  for
every check-in. But one thing I could do is release the first dated version
without a date if that helps. Just [14.6.3]. Would that somehow help? I'd
rather not do that, though.

On Tue, Aug 30, 2016 at 3:16 AM, Spencer Bliven <spencer.bli...@gmail.com>
wrote:

> I would advocate that maven should get a new artifact whenever sourceforge
> gets a new jar. For this reason I've been including the date as part of the
> version number. There is no way to silently replace a previous jar without
> giving it a new version number, so we can't just have a "14.6.2" branch
> that will get updated every week.
>
> I would just do a svn copy every time you push something to sourceforge.
> Probably there is a way to automate this in ant, but I'd have to look into
> it. Manually, something like
>
> svn copy http://svn.code.sf.net/p/jmol/code/branches/v14_6
> http://svn.code.sf.net/p/jmol/code/tags/v14_6_2_2016_08_28
>
> BTW, I'll be at the Web-based molecular graphics conference next week, so
> we can discuss details then if you want.
>
> -Spencer
>
> On Mon, Aug 29, 2016 at 7:45 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> I would not expect any Maven updates until there is an actual release, as
>> I did yesterday. What you are seeing there are minor bug fixes. If I can
>> tag those in some way, I'd be happy to do that.
>>
>> On Mon, Aug 29, 2016 at 7:42 AM, Spencer Bliven <spencer.bli...@gmail.com
>> > wrote:
>>
>>> Would it be possible to start creating tags for all releases? I think
>>> the last couple maven releases might have included a few commits more than
>>> they should have because I just used the head of the 14_6 branch. For
>>> instance, the "14.6.2_2016.08.28" on maven central was built from r21231.
>>> I'm not certain whether this matches the revision on sourceforge or whether
>>> one of the other five commits on 8-28-2016 would have been better. This
>>> would be much easier to track if the process of releasing to sourceforge
>>> included a tagging step.
>>>
>>> Thanks,
>>>
>>> Spencer
>>>
>>> 
>>> --
>>>
>>> ___
>>> Jmol-developers mailing list
>>> Jmol-developers@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>> 
>> --
>>
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
> 
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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
--
___
Jmol-developers mailing list
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Re: [Jmol-developers] load models {0 0 1} is broken in 14.6.0 seires

[Robert Hanson]

It's fixed.

On Wed, Jun 22, 2016 at 12:22 PM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:

> Thank you.
>
> Does this message means something to you? It’s from 14.6.0.
>
> script ERROR: TypeError: this.setShapeVisibility is not a function. (In
> 'this.setShapeVisibility(a,b)', 'this.setShapeVisibility' is undefined)
>
> Maybe not all files from the new version loaded properly?
>
> On 22 Jun 2016, at 7:14 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> Fixed. Will update at SVN later today or tonight.
>
> On Wed, Jun 22, 2016 at 10:52 AM, Angel Herráez <angel.herr...@uah.es>
> wrote:
>
>>
>> load models {0 0 1} filename
>>
>> is broken in all 14.6.0 releases; it complains the closing brace was not
>> expected
>>
>> We are trying to fix a problem in Proteopedia (Jmol 14.4.1) with
>> rendering of beta strands when the file does not contain SHEET
>> records(note*). I realized that bug is fixed in 14.6 so we planned to
>> upgrade Proteopedia, but now we cannot use 14.6 since loading 1st model is
>> a default script in Proteopedia
>>
>>
>>
>> Note *) rendering broken between 14.3.15_2015.06.19 correct and
>> 14.4.0_2015.11.06 broken. Correct again in 14.6.0
>>
>> Demo of the problem at first green link in
>> *http://proteopedia.org/w/User:Jaime.Prilusky/Test/green_link*
>> <http://proteopedia.org/w/User:Jaime.Prilusky/Test/green_link>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape___
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Re: [Jmol-developers] load models {0 0 1} is broken in 14.6.0 seires

[Robert Hanson]

Fixed. Will update at SVN later today or tonight.

On Wed, Jun 22, 2016 at 10:52 AM, Angel Herráez 
wrote:

>
> load models {0 0 1} filename
>
> is broken in all 14.6.0 releases; it complains the closing brace was not
> expected
>
> We are trying to fix a problem in Proteopedia (Jmol 14.4.1) with rendering
> of beta strands when the file does not contain SHEET records(note*). I
> realized that bug is fixed in 14.6 so we planned to upgrade Proteopedia,
> but now we cannot use 14.6 since loading 1st model is a default script in
> Proteopedia
>
>
>
> Note *) rendering broken between 14.3.15_2015.06.19 correct and
> 14.4.0_2015.11.06 broken. Correct again in 14.6.0
>
> Demo of the problem at first green link in
> *http://proteopedia.org/w/User:Jaime.Prilusky/Test/green_link*
> 
>
>
>
>
>
>
>
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Reloading current structure fails

[Robert Hanson]

Does seem odd. Here is a way to do it, though:


data "example"
2
testing
C 1 1 1
O 2 2 2
end "example";
load inline @{data("example")} {1 1 1} spacegroup 22 unitcell [3 4 5 90 90
90]

then  you can use

load ""

or

load inline @{data("example")}

any time. Or you could define

x = data("example")

then  use

load inline @x 


​
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
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Re: [Jmol-developers] application errors

[Robert Hanson]

You have to make sure you do

run as   and then select the "clean" option. You can't just use
Project...clean

Bob

On Fri, May 27, 2016 at 10:32 AM, Kanters, Rene <rkant...@richmond.edu>
wrote:

> I always thought that it 'cleaning' it means that it would remove all
> those files, which is why I was so surprised that it didn't do it. I guess
> it has something to do with what is in the build.xml file, but I have never
> understood the ant build files well enough to mess with those
>
> On May 27, 2016, at 10:30 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> yes, that's right. If you figure how to make "Project Clean" remove the
> build files, that would be  great. We could set that up.
>
> On Fri, May 27, 2016 at 9:10 AM, Kanters, Rene <rkant...@richmond.edu>
> wrote:
>
>> I decided to keep an eye on the build folder and noticed that when I did
>> a 'Clean' project the files were not removed. I did an rm -rf in there to
>> start fresh, did a build and now it works...
>>
>> René
>>
>> On May 27, 2016, at 9:05 AM, Kanters, Rene <rkant...@richmond.edu> wrote:
>>
>> Bob,
>>
>> I did clean builds several times to no avail. I am building the Jmol.jar
>> using an ant builder setup for the Properties of Jmol, where I specify it
>> to use Jmol/build.xml buildfile. I think that when I run it directly in
>> Eclipse is may use the Java Builder set up, but that one is not editable,
>> so I can't tell what exactly that does.
>>
>> I also did an 'override and update' to make sure that I pulled everything
>> back as it is on the SVN server. The only files I did not allow to
>> overwrite were the .externalToolBuilders/Jmol.jar.launch (which does not
>> seem to have a version in SVN, probably something new in Mars.2),
>> Settings/org.eclipse.jdt.core.pref and .project. (like I had before).
>>
>> I do indeed not see the org/jmol/api/JmolBioResolver (and am somewhat
>> surprised it isn't echoed as org.jmol.apl), so why is there a script that
>> still seems to know about that and only needs it when I am running the
>> Jmol.jar (using java -jar Jmol.jar) but not when I am running it from
>> within eclipse?
>>
>> René
>>
>> On May 27, 2016, at 1:44 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>>
>> JmolBioResolver was decommissioned. Perhaps you have not fully
>> synchronized. Try a clean build.
>>
>> I have also added those to the release branch, 14.6.
>>
>> On Thu, May 26, 2016 at 4:04 PM, Kanters, Rene <rkant...@richmond.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> I just synchronized after having made the changes in the qchem reader
>>> this morning, and now find that the application when running in the Eclipse
>>> Mars.2 (Release 4.5.2) run the app fine, but that the Jmol.jar I am
>>> creating gives an error message when I try to measure things using the
>>> console:
>>>
>>> $ measure (c2)(c6)
>>> script ERROR: java.lang.NoSuchMethodError:
>>> org.jmol.viewer.Viewer.getJBR()Lorg/jmol/api/JmolBioResolver;
>>>
>>> Does anybody have any idea why that started happening?
>>>
>>> René
>>>
>>>
>>>
>>> --
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data
>>> untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> ___
>>> Jmol-developers mailing list
>>> Jmol-developers@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>> --
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols
>&g

Re: [Jmol-developers] application errors

[Robert Hanson]

Search the src code for references to JmolBioResolver. There should be none.

delete the directories

bin
build/classes
build/applet-classes

and recompile.







On Fri, May 27, 2016 at 8:05 AM, Kanters, Rene <rkant...@richmond.edu>
wrote:

> Bob,
>
> I did clean builds several times to no avail. I am building the Jmol.jar
> using an ant builder setup for the Properties of Jmol, where I specify it
> to use Jmol/build.xml buildfile. I think that when I run it directly in
> Eclipse is may use the Java Builder set up, but that one is not editable,
> so I can't tell what exactly that does.
>
> I also did an 'override and update' to make sure that I pulled everything
> back as it is on the SVN server. The only files I did not allow to
> overwrite were the .externalToolBuilders/Jmol.jar.launch (which does not
> seem to have a version in SVN, probably something new in Mars.2),
> Settings/org.eclipse.jdt.core.pref and .project. (like I had before).
>
> I do indeed not see the org/jmol/api/JmolBioResolver (and am somewhat
> surprised it isn't echoed as org.jmol.apl), so why is there a script that
> still seems to know about that and only needs it when I am running the
> Jmol.jar (using java -jar Jmol.jar) but not when I am running it from
> within eclipse?
>
> René
>
> On May 27, 2016, at 1:44 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> JmolBioResolver was decommissioned. Perhaps you have not fully
> synchronized. Try a clean build.
>
> I have also added those to the release branch, 14.6.
>
> On Thu, May 26, 2016 at 4:04 PM, Kanters, Rene <rkant...@richmond.edu>
> wrote:
>
>> Hi,
>>
>> I just synchronized after having made the changes in the qchem reader
>> this morning, and now find that the application when running in the Eclipse
>> Mars.2 (Release 4.5.2) run the app fine, but that the Jmol.jar I am
>> creating gives an error message when I try to measure things using the
>> console:
>>
>> $ measure (c2)(c6)
>> script ERROR: java.lang.NoSuchMethodError:
>> org.jmol.viewer.Viewer.getJBR()Lorg/jmol/api/JmolBioResolver;
>>
>> Does anybody have any idea why that started happening?
>>
>> René
>>
>>
>>
>> --
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data
>> untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> 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
>
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports.
> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


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


If nature does not ans

Re: [Jmol-developers] myJmol as variable in Jmol.script

[Robert Hanson]

yes, if you check

show orientation

you will see a parameter "rotation radius"

You can set that to a new number, then disable zoom. It sets the
magnification for "100%".



​
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: [Jmol-developers] commit with localization files

[Robert Hanson]

great -- that's all now in the release branch as well.

On Thu, May 19, 2016 at 6:00 PM, Angel Herráez  wrote:

> Forget that last one -- I found where the language must be added,
> src\org\jmol\i18n\Language.java
>
> I am adding Russian since it is over 95% translated
>
>
>
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>



-- 
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
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] myJmol as variable in Jmol.script

[Robert Hanson]

Klaus,

When you create an applet, it automatically creates a top-level object with
the name of your applet.

However, you can't do anything with that object until it is at least
started to be created.

Have you tried any of the html files in the jsmol/ directory? There are
plenty of examples of this. One  that comes to mind is
http://chemapps.stolaf.edu/jmol/jsmol/simple2_old.htm


I do not recommend eval(name), and I have never needed it.


On Mon, May 9, 2016 at 2:25 AM, Klaus Schaper  wrote:

> Hi everybody,
>
>
>
> Thanks to Rolf, that did the trick! I successfully converted a little bit
> of script to the new syntax and the other functions will hopefully cause no
> problems.
>
>
>
>
>
> However, one more problem remains. After converting the script to the new
> syntax using
>
>
>
> 1) Jmol.getApplet(Ziel, Info);
>
>
>
> and
>
>
>
> 2) Jmol.script(eval(name), commands);
>
>
>
> The code will run in my JSmol enviiroment, but not in the Jmol environment.
>
>
>
> My conclusion is, that
>
> either the new syntax is not compatible to the old Jmol using JAVA,
>
> or that I did not include all necessary files in my html document. Which 
> files (beside the old Jmol.js) do I have to include?
>
>
>
> Klaus
>
>
>
>
>
>
>
>
> 
>
>
>
> PD Dr. Klaus Schaper
>
>
>
> http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de
>
>
>
> e-mail: scha...@klaus-schaper.de
>
>
>
> Arbeitsgruppe für Organische Photochemie
>
> Institut für Organische Chemie und Makromolekulare Chemie I
>
> Raum 26.43.00.27
>
>
>
> Heinrich-Heine-Universität Düsseldorf
>
> Universitätsstr. 1
>
> D-40225 Düsseldorf
>
> Deutschland
>
>
>
> Telefon: +49 211 81 12571
>
> FAX: +49 211 81 14324
>
>
>
>
> 
>
>
>
>
>
>
> --
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] myJmol as variable in Jmol.script

[Robert Hanson]

I would put a line

alert(name)

in that function to see what that variable is. Perhaps it is not defined at
the time you are making  the call.


Also, I don't  recommend giving an applet a name like "A" or "B" -- to easy
to use a variable that is used by something else. I would suggest "jmolA"
"jmolB" or something like that. What most people do is "jmolApplet1"
"jmolApplet2" .

Bob



​
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[Jmol-developers] build problems in Eclipse Mars

[Robert Hanson]

Continuing this discussion from a bug fix.

Rene, I have to ask: Are you running build.xml, not build-eclipse.xml?

Build-eclipse.xml is just for running within Eclipse, I think. No Jar file
created. Could it be as simple as that?

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
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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Re: [Jmol-developers] Java 9 issue

[Robert Hanson]

OK. No rush, I think.

On Thu, Feb 18, 2016 at 4:29 PM, Nicolas Vervelle <nverve...@gmail.com>
wrote:

>
>
> On Thu, Feb 18, 2016 at 8:52 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Angel, it's just that the gtext processor is set up for "_" -- I guess,
>> though, that must just be a setting. We liked "_" because it was so short,
>> and actually that does help in keeping file sizes as low as possible.  So,
>> Nico, I guess it is this, right?
>>
>>   
>>
>
> Yes, it's how you can configure gettext to find the translatable strings.
> It's in 2 places in build-i18n.xml, once for Jmol.pot, once for
> JmolApplet.pot.
>
> Nico
>
>
>
>>
>>
>> On Thu, Feb 18, 2016 at 4:28 AM, Angel Herráez <angel.herr...@uah.es>
>> wrote:
>>
>>> if I may throw a suggestion, "L10N" is a term commonly associated to
>>> localization
>>>
>>> It could also be used for the current "idioma" folder in the jsmol
>>> package (I
>>> am happy with idioma, but others may not understand what it is for)
>>>
>>>
>>>
>>>
>>> --
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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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
>>
>>
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
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>> ___
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>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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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-developers] Java 9 issue

[Robert Hanson]

Angel, it's just that the gtext processor is set up for "_" -- I guess,
though, that must just be a setting. We liked "_" because it was so short,
and actually that does help in keeping file sizes as low as possible.  So,
Nico, I guess it is this, right?

  


On Thu, Feb 18, 2016 at 4:28 AM, Angel Herráez  wrote:

> if I may throw a suggestion, "L10N" is a term commonly associated to
> localization
>
> It could also be used for the current "idioma" folder in the jsmol package
> (I
> am happy with idioma, but others may not understand what it is for)
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140
> ___
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> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>



-- 
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-developers] problem parsing DNA from assembly mmCIF (PDBe)

[Robert Hanson]

What is the difference between loading an "assembly" and FILTER
"biomolecule 1" ? Is there some advantage to loading the assembly? I have
never looked at those files.



On Thu, Jan 28, 2016 at 5:33 AM, Angel Herráez  wrote:

> We are starting to work on reading mmCIF files from PDBe, for "assemblies".
> This means the actual biological unit of the molecule, be it monomer,
> dimer,
> tetramer, etc -- manually checked since there are often several
> automatically
> prepared biological units in PDB
>
> Apparently EBI has been applying some variation in which CIF dta fields are
> retained in the assemby CIF file
> So far we have managed (Proteopedia) to handle those idiosyncrasies, but I
> have hit some weird problem with 2LEV
> It has protein + DNA, several models.
> Jmol 14.4.1 Jan 15 fails to render the DNA at all
>
> These are my checks:
>
> load http://www.ebi.ac.uk/pdbe/entry-files/download/pdb2lev.ent
> // PDB file -- ok
>
> load
>
> http://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divide
> d/pdb/le/pdb2lev.ent.gz
> // PDB file (gz) -- ok
>
> load http://www.ebi.ac.uk/pdbe/entry-files/download/2lev_updated.cif
> // Updated mmCIF file -- ok
>
> load
> http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
> // Assembly 1 (mmCIF; gz) -- DNA is not displayed
> select dna  //19040 atoms selected
> hide all  //37340 hidden atoms
> display all  //0 hidden atoms
> // in all cases, no rendering of DNA
>
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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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-developers] problem parsing DNA from assembly mmCIF (PDBe)

[Robert Hanson]

The DNA strands are there, but they are coming in as individual models. So
we have 60 models (protein + 2 DNA strands) instead of 20 in that assembly
file. It seems to be because the models are not in order. The sequence in
the file goes

 protein  models 1-20
 dna strand models 1-20
 dna strand models 1-20

Jmol is not set up to do that. So when it hits a new model, it assigns a
new number. I'm surprised, though, that it is losing the PDB model number
in the file. I will check to see if there is something we can do about
that. It's also possible that we could re-order those.



On Thu, Jan 28, 2016 at 5:33 AM, Angel Herráez  wrote:

> We are starting to work on reading mmCIF files from PDBe, for "assemblies".
> This means the actual biological unit of the molecule, be it monomer,
> dimer,
> tetramer, etc -- manually checked since there are often several
> automatically
> prepared biological units in PDB
>
> Apparently EBI has been applying some variation in which CIF dta fields are
> retained in the assemby CIF file
> So far we have managed (Proteopedia) to handle those idiosyncrasies, but I
> have hit some weird problem with 2LEV
> It has protein + DNA, several models.
> Jmol 14.4.1 Jan 15 fails to render the DNA at all
>
> These are my checks:
>
> load http://www.ebi.ac.uk/pdbe/entry-files/download/pdb2lev.ent
> // PDB file -- ok
>
> load
>
> http://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divide
> d/pdb/le/pdb2lev.ent.gz
> // PDB file (gz) -- ok
>
> load http://www.ebi.ac.uk/pdbe/entry-files/download/2lev_updated.cif
> // Updated mmCIF file -- ok
>
> load
> http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
> // Assembly 1 (mmCIF; gz) -- DNA is not displayed
> select dna  //19040 atoms selected
> hide all  //37340 hidden atoms
> display all  //0 hidden atoms
> // in all cases, no rendering of DNA
>
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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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-developers] Escape.e function misidentifying P4 types as T3...

[Robert Hanson]

It's an ordering issue. Yes, P4 subclasses T4, which subclasses T3. I'll
fix it.

On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow  wrote:

> It appears that at line 117 in Escape.java, type P4 objects are being
> misidentified as type T3.  This means that the value of the "w" subtype is
> not being returned as part of the returned text vector only "x", "y" and
> "z".  I noticed this because it breaks the surface tool which uses P4
> objects to define planes.
>
> It is not clear to me why this is happening.  Is P4 type a subtype of T3?
>
> Jonathan
>
> --
>Dr. Jonathan H. Gutow
> Chemistry Department gu...@uwosh.edu
> UW-OshkoshOffice:
> 920-424-1326
> 800 Algoma Boulevard FAX:920-424-2042
> Oshkosh, WI 54901
>http://www.uwosh.edu/facstaff/gutow/
>
>
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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-developers] Escape.e function misidentifying P4 types as T3...

[Robert Hanson]

I checked in a new Escape.java, which I guess fixes the problem. Do an
update on that, Jonathan. I guess we could leave the SurfaceTool the way it
is then.

On Wed, Dec 30, 2015 at 10:46 AM, Robert Hanson <hans...@stolaf.edu> wrote:

> In SurfaceTool.java, this:
>
>   cmd.append(" plane ").append(Escape.e(plane))
>
>
> should read:
>
>   cmd.append(" plane ").append(Escape.eP4(plane))
>
> similar with:
>
> .append(Escape.e(slice.leftPlane));
> .append(Escape.e(slice.rightPlane));
>
> and in Escape.java:
>
> if (x instanceof T3)
>   return eP((T3) x);
> if (x instanceof P4)
>   return eP4((P4) x);
>
>
> should read
>
> if (x instanceof P4)
>   return eP4((P4) x);
> if (x instanceof T3)
>   return eP((T3) x);
>
>
> On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:
>
>> It appears that at line 117 in Escape.java, type P4 objects are being
>> misidentified as type T3.  This means that the value of the "w" subtype is
>> not being returned as part of the returned text vector only "x", "y" and
>> "z".  I noticed this because it breaks the surface tool which uses P4
>> objects to define planes.
>>
>> It is not clear to me why this is happening.  Is P4 type a subtype of T3?
>>
>> Jonathan
>>
>> --
>>Dr. Jonathan H. Gutow
>> Chemistry Department gu...@uwosh.edu
>> UW-OshkoshOffice:
>> 920-424-1326
>> 800 Algoma Boulevard FAX:920-424-2042
>> Oshkosh, WI 54901
>>http://www.uwosh.edu/facstaff/gutow/
>>
>>
>> --
>>
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> 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
>
>


-- 
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-developers] Escape.e function misidentifying P4 types as T3...

[Robert Hanson]

Go ahead the change that Escape.e to Escape.eP4 anyway, and check that in
if you want.

On Wed, Dec 30, 2015 at 3:02 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:

> I can verify that the reordering fixed the problem.
>
> Jonathan
>
> On Wed, Dec 30, 2015 at 10:50 AM, Robert Hanson <hans...@stolaf.edu>
> wrote:
>
>> I checked in a new Escape.java, which I guess fixes the problem. Do an
>> update on that, Jonathan. I guess we could leave the SurfaceTool the way it
>> is then.
>>
>> On Wed, Dec 30, 2015 at 10:46 AM, Robert Hanson <hans...@stolaf.edu>
>> wrote:
>>
>>> In SurfaceTool.java, this:
>>>
>>>   cmd.append(" plane ").append(Escape.e(plane))
>>>
>>>
>>> should read:
>>>
>>>   cmd.append(" plane ").append(Escape.eP4(plane))
>>>
>>> similar with:
>>>
>>> .append(Escape.e(slice.leftPlane));
>>> .append(Escape.e(slice.rightPlane));
>>>
>>> and in Escape.java:
>>>
>>> if (x instanceof T3)
>>>   return eP((T3) x);
>>> if (x instanceof P4)
>>>   return eP4((P4) x);
>>>
>>>
>>> should read
>>>
>>> if (x instanceof P4)
>>>   return eP4((P4) x);
>>> if (x instanceof T3)
>>>   return eP((T3) x);
>>>
>>>
>>> On Tue, Dec 29, 2015 at 7:59 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:
>>>
>>>> It appears that at line 117 in Escape.java, type P4 objects are being
>>>> misidentified as type T3.  This means that the value of the "w" subtype is
>>>> not being returned as part of the returned text vector only "x", "y" and
>>>> "z".  I noticed this because it breaks the surface tool which uses P4
>>>> objects to define planes.
>>>>
>>>> It is not clear to me why this is happening.  Is P4 type a subtype of
>>>> T3?
>>>>
>>>> Jonathan
>>>>
>>>> --
>>>>Dr. Jonathan H. Gutow
>>>> Chemistry Department gu...@uwosh.edu
>>>> UW-OshkoshOffice:
>>>> 920-424-1326
>>>> 800 Algoma Boulevard FAX:920-424-2042
>>>> Oshkosh, WI 54901
>>>>http://www.uwosh.edu/facstaff/gutow/
>>>>
>>>>
>>>> --
>>>>
>>>> ___
>>>> Jmol-developers mailing list
>>>> Jmol-developers@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>>
>> --
>>
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
>Dr. Jonathan H. Gutow
> Chemistry Department gu...@uwosh.edu
> UW-OshkoshOffice:
> 920-424-1326
> 800 Algoma Boulevard FAX:920-424-2042
> Oshkosh, WI 54901
>http://www.uwosh.edu/facstaff/gutow/
>
>
> --
>
> ___
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
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-developers] Interfacing Jmol with Oculus Rift VR

[Robert Hanson]

First thing you should think about is using

set navigationMode

This gives an "immersion" perspective that may be closest to your needs. See

http://chemapps.stolaf.edu/jmol/docs/misc/navigation.pdf

for ideas.

​
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Re: [Jmol-developers] Interfacing Jmol with Oculus Rift VR

[Robert Hanson]

You probably should be interacting via a port using the SYNC command.
However, I don't think navigation mode was ever set up for that. In lieu of
that, you should use script commands. Otherwise your asynchronous calls
will not be thread safe, I think.

Take a close look at that document and see if your parameters are
translatable into that.




On Tue, Dec 8, 2015 at 6:51 AM, Zhezheng Chen <chrischen1...@gmail.com>
wrote:

> I've already tried the navigation mode. I put the position 3d vector from
> Oculus to TransformManager.navX, TransformManager.navY and
> TransformManager.navZ but it didn't work. So I doubt if it's right to just
> use functions like TranformManager.setNavigationXYZ.
>
> Any other ways to navigate?
>
> On Tue, Dec 8, 2015 at 8:04 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> First thing you should think about is using
>>
>> set navigationMode
>>
>> This gives an "immersion" perspective that may be closest to your needs.
>> See
>>
>> http://chemapps.stolaf.edu/jmol/docs/misc/navigation.pdf
>>
>> for ideas.
>>
>> ​
>>
>>
>> --
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140
>> ___
>> Jmol-developers mailing list
>> Jmol-developers@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140
> ___
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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-developers] SVN access problem

[Robert Hanson]

I support this idea in principle; I just started using Git on another
project (Jalview), and I certainly see the advantages. No system is immune
to failure, but it is true that the local repository aspect of Git does
mean there cannot be a catastrophic failure that impacts us for weeks the
way we just had with SF. (I think that is up; I just made a test commit.)

I have had problems with line endings, and I have had a lot of problems
with overriding changes when that is necessary. We would need to make sure
everyone moves to Eclipse 4.5. I'm reticent to do that just now myself,
because it's a path of no return, or at least one would have to re-check
out projects all over again (and I have quite a few of those at this
point).

We would have to do this very carefully.

Bob


On Tue, Jul 28, 2015 at 5:00 PM, Andreas Prlic andr...@sdsc.edu wrote:

 I'd strongly support a move to github. It is so much better in so many
 ways...

 Andreas

 On Mon, Jul 27, 2015 at 12:41 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 Perhaps  time to move to GitHub? (not sure about the limitations)

 On Mon, Jul 27, 2015, 13:24 Nicolas Vervelle nverve...@gmail.com wrote:

 On Mon, Jul 27, 2015 at 1:11 PM, Michael Banck mba...@debian.org
 wrote:

 On Mon, Jul 27, 2015 at 01:02:17PM +0200, Nicolas Vervelle wrote:
  SVN access should have been restored this weekend by sourceforge.

 I heard some project lost a couple of SVN revisions because the backup
 did not contain the latest state of affairs.

 Just as a word of warning.


 Yes, apparently about 500 projects are in this situation.
 For those projects, sourceforge should have sent a mail to the the
 project administrator, titled SourceForge SVN repository data gap
 notification for project 
 I received one for a project, but not for Jmol.
 Hopefully, that means that Jmol SVN is completely restored.

 Nico



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Re: [Jmol-developers] Changing Console Location and Adding a New Menu

[Robert Hanson]

Actually, it is


div id=jmolApplet0_console
style=background-color:blue;width:700px;height:400px;overflow:auto/div



On Mon, Jun 29, 2015 at 11:01 AM, Robert Hanson hans...@stolaf.edu wrote:

 Note that I assumed you meant the Jmol console that comes up with the


 console


 command. If you meant the information that is behind the applet, then that
 is simply in Info use

   console:consolediv

 and then use something like:

 div id=consolediv
 style=background-color:blue;width:400px;height:300px;overflow:auto/div




 On Tue, Jun 23, 2015 at 9:33 AM, Sam Blackman sa.blackma...@gmail.com
 wrote:

 Hello Jmol Devs,

 I'm looking at changing the location of the console so that it is not
 a separate window and instead at the bottom of the main Jmol GUI. I'm
 wondering where I can find the main GUI in order to add the console to it
 (in the source code). In addition, I'm also trying to add a separate GUI
 menu that runs when Jmol opens (for experimental purposes). If this is the
 wrong email to be emailing, I do apologize.

 Cheers,
 Sam


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


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Re: [Jmol-developers] CrystalReader and external pressure

[Robert Hanson]

found it. Fixed. See

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.07.07b.zip (uploading
shortly)

On Tue, Jul 7, 2015 at 8:49 AM, Georg Eickerling 
georg.eickerl...@physik.uni-augsburg.de wrote:

 Dear all,

 this is a feature request for the CrystalReader of jmol. When doing
 optimizations employing external pressure with CRYSTAL, the output contains
 some additional lines starting with the string TOTAL ENERGY which jmol
 can
 not cope with at the moment:


 TOTAL ENERGY CORRECTED: EXTERNAL STRESS CONTRIBUTION =0.944E+00

 TOTAL ENERGY(DFT)(AU)( 27) -1.2874392471314E+04 DE (AU)   -5.323E-04

 jmol does this ATM in src/org/jmol/adapter/readers/xtal/CrystalReader.java

 line 239:

 if (line.startsWith( TOTAL ENERGY)) {
   readEnergy();
   rd();
   if (line.startsWith( ))
 discardLinesUntilContains(SYMMETRY ALLOWED);
   else if (line.startsWith( ))
 discardLinesUntilContains2(PREDICTED ENERGY CHANGE, HHH);
   return true;
 }


 This will crash if the first of the above lines is present in addition to
 the
 second as most likely readEnergy can not parse the EXTERNAL STRESS stuff.

 I am completely illiterate when it comes to java and even fail to build
 jmol
 from the src using ant on Debian Jessie, so unfortunately I can not
 provide the
 required 2-line fix to simply skip all the EXTERNAL STRESS lines in this
 case.

 regards

 Georg



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Re: [Jmol-developers] xml files?

[Robert Hanson]

Sam, I see this thread now. Those ANT tasks are only for the release
version of Jmol. You   are welcome to do this. Ideally we would incorporate
your modifications into a future release of Jmol. It is highly modular for
this very purpose.

You need the corresponding _11, _12, and _13 tasks, not _01/_02/_03

You will need three projects checked out:

Jmol - checked out as Jmol - the TRUNK version (Jmol 13.3), recently
checked out. No development should be done on the stable branch (Jmol
13.2). There is daily active development on this trunk.

JSmol - checked out and up to date. (actively developed)

JSpecView - needed for build_12, even if you do not need it. It is actually
two check-outs, one for JSpecView and one for JSpecViewLib. (This one is
stable; no work on this recently.)

You must use one of the versions of the Java2Script Eclipse plug in that
you find in JSmol/j2s/eclipse-plugin, which are up-to-date versions of J2S.

JSmol does not use the standard J2S JavaScript pieces. Those are all in the
JSmol project.

Bob Hanson
principal developer, Jmol




On Wed, Jul 1, 2015 at 10:23 AM, Sam Blackman samuel.black...@nist.gov
wrote:

 But do you know if Jmol Developers had to change Java2Script in order
 for it to work properly?

 -Sam

 On 07/01/2015 12:21 PM, Angel Herráez wrote:
  I am trying to convert the Jmol source code to JSmol using Java2Script.
  I've made some changes to it and I want to know how they affect JSmol. I
  got the code from here: http://jmol.sourceforge.net/#Obtain%20Jmol
  Ah, ok
  That's a purely developer-programmer issue, then. It's clear now.
 
  I cannot help on that, sorry.
 
 
 
 
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Re: [Jmol-developers] Changing Console Location and Adding a New Menu

[Robert Hanson]

Good idea. I have modified JmolCore.js and JmolConsole.js such that you can
now add a div:

// BH 6/29/2015 9:50:21 AM adds option for user to set console as a div on
a page.
//as jmolApplet0_console where jmolApplet0 is the id of the applet.
//   for example: div id=jmolApplet0_console
style=width:600px;height:362px/div

and will get that out later today.


On Tue, Jun 23, 2015 at 9:33 AM, Sam Blackman sa.blackma...@gmail.com
wrote:

 Hello Jmol Devs,

 I'm looking at changing the location of the console so that it is not
 a separate window and instead at the bottom of the main Jmol GUI. I'm
 wondering where I can find the main GUI in order to add the console to it
 (in the source code). In addition, I'm also trying to add a separate GUI
 menu that runs when Jmol opens (for experimental purposes). If this is the
 wrong email to be emailing, I do apologize.

 Cheers,
 Sam


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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
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Re: [Jmol-developers] Right click menu

[Robert Hanson]

you can drag it anywhere on the screen just by clicking on a separator and
dragging; it will always come up at the point you clicked, though.

On Fri, Jun 26, 2015 at 1:31 PM, Sam Blackman sa.blackma...@gmail.com
wrote:

 Hello all,
  Would it be possible to make the right click menu in it's own frame (like
 the console) so that it could be dragged around anywhere on the screen?

 Cheers,
 Sam


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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
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Re: [Jmol-developers] DOCUMENTATION AnimFrameCallback

[Robert Hanson]

Actually, it was a bug in JSmol in not delivering all the parameters. In
fact, there are eleven parameters, including

data = new Object[] { htmlName,
Integer.valueOf(Math.max(frameNo, -2 - frameNo)),
Integer.valueOf(fileNo), Integer.valueOf(modelNo),
Integer.valueOf(Math.abs(firstNo)),
Integer.valueOf(Math.abs(lastNo)),
Integer.valueOf(isAnimationRunning ? 1 : 0),
Integer.valueOf(animationDirection),
Integer.valueOf(currentDirection),
data[2]/*entryName*/, data[3]/*morphModel*/

entryName is the name that is at the top of the window in the Jmol applet.
morphModel is a floating point number that might  show  some intermediate
value
between two frames, indicating the fractional point between the two actual
frames that the morph is calculated from.

On Wed, Jun 17, 2015 at 4:56 AM, Angel Herráez angel.herr...@uah.es wrote:

 Dear Bob,

 http://chemapps.stolaf.edu/jmol/docs/#setcallback
 set AnimFrameCallback
 says 9 parameters are returned. I only see 8; I think that maybe
 isAnimationRunning and animationDirection are merged into one?

 14.2.14_2015.06.11

 Regards,
 Angel



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Re: [Jmol-developers] Script debugging problem

[Robert Hanson]

On Fri, Apr 17, 2015 at 6:44 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 Hi all,

 I have some problems debugging a complex script in Jmol.

 First of all, the command 'set scriptReportingLevel' doesn't seem to
 work in Jmol 14.3.13_2015.04.08. It is always setting the value to zero.

 Q: What do the numbers (e.g.: $[2.295.299]) in the debugging output
 after the command 'set showScript on' mean?


$ on first line indicates that this script should read these lines with
$[...] and not others
2  script level
295 line number, without comments
299 command number

The problem with early exit of a function was a misplaced line of code.
This would also have the same effect on other surrounding contexts, such as
if, for, do, and while, so perhaps that was the whole issue.

The previous fix did fix a problem that using an empty array in a for
statement resulted in the loop being run anyway. That's not the case now.

Interesting observation about

x = {:}

print x[]

being the same as

x = {A:3}

print x[]

I guess we have to live with that. Jmol doesn't have a null variable. The
default for undefined is just an empty string.

see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.04.17.zip

Jmol.___JmolVersion=14.3.13_2015.04.16

bug fix: for in/from broken in 14.3.13_2015.04.05
 -- entering a FOR loop with empty has pops {...} context one level too
far, exiting functions














 The first number looks like it could be the function call level.
 The third number could be the line number within the function after
 removing empty lines.

 Following the debugging information for a problematic function (~500
 lines of code, see short extract below) the critical line seems to be a
 'for' loop. Depending on the input data the loop sometimes cycles more
 often (twice instead of once) than indicated by the variable value
 ('fileCount=1' in any of the described cases) or the function is exited
 (without any error message or exception) after reaching the line the
 second time:

 $[2.83.82] for (var fileNumber=1; fileNumber=fileCount; fileNumber++);
 $[2.400.400]
 $[2.83.82] for (var fileNumber=1; fileNumber=fileCount; fileNumber++);

 --- Problematic function, extract ---
 function parseNetworkTsvData(dataHashref) {
...
if (fileCount 0) {
  for (var fileNumber=1; fileNumber=fileCount; fileNumber++) {
...
  }
  ...
}
...
 }
 -

 Replacing the old syntax by the new one for (var fileNumber FROM [1
 fileCount]) { dosen't change the problematic behaviour. The only
 visible difference can be seen in the case of the additional loop run.
 With the old syntax 'fileNumber' is 1 in the first cycle and 2 in
 the second one. With the new syntax it is 1 during both cycles.

 Although I have no clue what difference between the datasets is
 responsible for the different behaviour (they have many differences) it
 seems to be reproducible for each dataset.

 Since there might be involved some strange interference between the
 'for' loop and other block-level  elements I have added below also a
 version of the function reduced to all block-level begins/ends.

 Regards,
 Rolf

 --- Problematic function, larger extract ---
 function parseNetworkTsvData(dataHashref) {
if (dataHashref.type != hash) {
} else {
  if (networkType == ) {
  }
  if (dataHashref..subsets.type != hash) {
  } elseif (dataHashref..subsets.[dataHashref..currentSubsetKey].type
 != hash) {
  }
  if (dataHashref..networkDefinitions.type != hash) {
  } else {
if (dataHashref..networkDefinitions.[networkType].type != hash) {
} else {
  if
 (dataHashref..networkDefinitions.[networkType]..nodeColumns.type !=
 hash) {
if
 (dataHashref..networkDefinitions.[networkType]..nodeColumns.type !=
 hash) {
}
  }
}
  }
  if (dataHashref..tsvData.type != array) {
  }
}
if (msg != ) {
}
if (fileCount 0) {
  if (networkDefs..annotationColumns.type == hash) {
  }
  if (allNodes..nodeInfo.type != hash) {
  }
  if (allNodes..edgeInfo.type != hash) {
  }
  if (allNodes..edgeKeysUsed.type != hash) {
  }
  if (allNodes..neighbours.type != hash) {
  }
  for (var fileNumber=1; fileNumber=fileCount; fileNumber++) {
if (dataHashref..tsvData.[fileNumber].type == hash) {
  if (tsvData.type == array) {
if (rowCount  0) {
  for (var column in tsvData[1].keys) {
if (networkType == generic) {
  if (columnDefs.[column].type != hash) {
  }
}
if (nodeColumns[column]) {
  if (columnDefs[column].type != hash) {
  } else {
if (nodeTypesFound[nodeType].type != hash) {
}
if 

Re: [Jmol-developers] User-defined atom property type restriction

[Robert Hanson]

On Tue, Apr 14, 2015 at 3:43 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 04/13/2015 10:08 PM, Robert Hanson wrote:
  just the way it was implemented. But you can set atomName, atomType, and
  format in order to add string data to atoms. I'm sure that's not at all
  clear from the documentation.
 
 Since 'atomName' and 'atomType' are used internally (e.g. for
 determining Van der Waals radius or backbone atoms) one should rather
 not mess around with these properties.


good point.


 And the label is mainly intended (and needed) for providing information
 to the user. And even if one could use it for other purposes it would
 still be only a single additional property.

 One could of course use an associative array for storing extra
 information. But the advantage of storing them as user-defined atom
 properties would be to be able to make use of the advanced atom
 selection capabilities of Jmol also for these properties.


That really is the way to go.

$ load $caffeine
$ x = [test here]
$ y = select(z;{*};x[z.atomno] = test)
$ print y
({0})




 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
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Re: [Jmol-developers] User-defined atom property type restriction

[Robert Hanson]

just the way it was implemented. But you can set atomName, atomType, and
format in order to add string data to atoms. I'm sure that's not at all
clear from the documentation.

Bob


On Mon, Apr 13, 2015 at 11:07 AM, Rolf Huehne rhue...@fli-leibniz.de
wrote:

 Hi Bob and others,

 the documentation isn't very clear about it but it seems that
 user-defined atom properties can only be floating point numbers but not
 strings, integer numbers or boolean values in Jmol 14.3.13_2015.04.08.

  Examples ---
 load =1deh;
 {atomno=1}.property_test1=string;
 {atomno=1}.property_test2=5;
 {atomno=1}.property_test3=0.04;
 {atomno=1}.property_test4=false;
 print test1= + {atomno=1}.property_test1;
 print test2= + {atomno=1}.property_test2;
 print test3= + {atomno=1}.property_test3;
 print test4= + {atomno=1}.property_test4;

 --- Example Output 
 test1=NaN
 test2=5.0
 test3=0.04003
 test4=NaN
 ---

 Q: Is there a specific reason why only floating point numbers seem to be
 possible or were the other types just not implemented (yet)?

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

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

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 VAT No: DE 153 925 464
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 Tax Number: 162/141/08228



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If nature does not answer first what we want,
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[Jmol-developers] 20,000 commits

[Robert Hanson]

Just noticed that we are at revision # 20,448.

-- 
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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-developers] Loop speed optimization potential

[Robert Hanson]

On Wed, Apr 8, 2015 at 4:48 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:


 Q: Does 'i' contain the hash key (as in Perl) or the value?


the  key
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Re: [Jmol-developers] Loop speed optimization potential

[Robert Hanson]

Rolf, I think you could have a lot of fun  with the JavaScript functions
Jmol provides. Jmol never does loops like that. Instead it initializes a
three-dimensional binary tree -- we call it a binary forest :)  -- and
you specify a point and a radius, then iterate until done. It is far far
faster. The class is java.bspt.Bspf. It could be used outside of Jmol, I
think.

I did some minor tweaks of the FOR command, and I also added what I think
is a nice syntax that loops 2-3 times faster than (i=1; i  n; i++)

for (var i FROM [1 1] ) {
...increments up
}

for (var i FROM [10 -1]) {
...increments down
}

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.04.05.zip


Jmol.___JmolVersion=14.3.13_2015.04.05

code: rewriting FOR loop code to enhance performance

new feature: set showScript -1
  -- turns off history (on when commands come from the keyboard)
  -- stops every-second JavaScript interruptions -- Caution!

new feature: for (var i FROM [a, b]) {...}
  -- same as for (var i = a; i = b; i++) when a  b
  -- same as for (var i = a; i = b; i--) when a  b
  -- much more efficient

bug fix: for (var i in hashArray) {}  broken (also in 14.2; not fixed
there)











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Re: [Jmol-developers] accessing atom info

[Robert Hanson]

That's right. So that call is telling Jmol that there is a callback
listener. So now look for implementations of JmolCallbakListener. You will
find:


public class AppConsole extends JmolConsole ...
public abstract class JmolConsole extends GenericConsole ...
public abstract class GenericConsole implements JmolAppConsoleInterface,
JmolCallbackListener

There it is! You just make a class implement JmolCallbackListener and then
do in that class whatever you want to do to intercept those callbacks the
way GenericConsole does.

Note that it is not a callback distribution -- there is only one
JmolCallbackListener allowed -- if you want more, you need to implement
that yourself from that one class.

Bob


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Re: [Jmol-developers] Loop speed optimization potential

[Robert Hanson]

Rolf, you are definitely pushing the limit there, I think. What exactly
happens inside the loop you are really interested in using? If it is
anything much, then the looping itself is going to be insignificant
compared to the other processing.

I probably will regret suggesting this, but something to consider might be
a hybrid, where you retrieve key Jmol variables into JavaScript, run
whatever in Javascript, then put them back (if desired). The example below
is for an integer:

script
var _vi = jmolApplet0._applet.viewer.g.htUserVariables.get(i)
var i = _vi.intValue
// Object { index: 2147483647, flags: 3, myName: i, tok: 2, intValue: 0 }
// then do anything with that you want, and finally
_vi.intValue = 
/script

Other Jmol types will work -- after all, it's *all *JavaScript. (This could
not be done with the Java applet, of course.)

Jmol variable types include

  public final static int integer=  2;
  public final static int decimal=  3;
  public final static int string =  4;

  public final static int hash   =  6;  // associative array; Hashtable
  public final static int varray =  7;  // ListScriptVariable
  public final static int point3f=  8;
  public final static int point4f=  9;
  public final static int bitset =  10;

  public final static int matrix3f   = 11;
  public final static int matrix4f   = 12;
  public final static int listf  = 13;   // listf list-float is
specifically for xxx.all.bin,
  public final static int context= 14;
  public final static int barray = 15; // byte array


Believe it or not, you can change variables from one type to another this
way, though I would not necessarily recommend doing that.

var _vi = jmolApplet0._applet.viewer.g.htUserVariables.get(i);
var i = _vi.intValue;
_vi.tok = 2; // now Jmol's i variable is a float!
_vi.value = new Float(i);

The Jmol JAVASCRIPT command could be used to mix and match Jmol scripting
with JavaScript.

Mind you, _applet.viewer.g.htUserVariables  is NOT a public entity -- I
reserve the right to change its name at any time!

​Bob
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Re: [Jmol-developers] accessing atom info

[Robert Hanson]

What have you been able to learn from Integration.java? How does it work?

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Re: [Jmol-developers] Alternative nested array element access syntax

[Robert Hanson]

Interesting idea. Rolf. Are you aware of Jmol's recently added .. notation?

x = {a: {1: [x, y, z], 2: [I, II]}}

print x
print x..a
print x..a..1
print x..a..1..2

Does that satisfy your needs? It is only for regular arrays or associative
arrays with simple keys. You can't do this:

print x..testing here

for that you still need

print x[testing here]

(Just as in JavaScript.)

Personally, I would not like to try to build Perl-like syntax into Jmol.
Overall it is very unlike C++ or Java or JavaScript, and I've tried to keep
as close to those as possible. In Perl I believe the - notation is for *array
references:*

my @array = (1, 2, 3, 'four');
my $reference = \@array;
print $reference-[0];

not actual array names, right? You can't do this:

my @array = (1, 2, 3, 'four');
print $array-[0];

right? So I would prefer not to add that confusion to the mix.

Ambiguity of ranges: It's not that there is any ambiguity. I assure you
that is not the case. But Jmol's notation is a bit idiosyncratic, I admit.
The fact that the first model in a file was always 1 led me to develop 1
as the base for array elements. Was it a good choice? Maybe not. But that's
what we have. And the fact that we often want the last model suggested then
that [0] could mean the last rather than the first. And so we have
ranges such as a[3][-3]. It's not ambiguous. But it is multipurpose. So, as
you point out, for associative arrays, a[1][1] is not a range. (What would
a range in an associative array mean, after all.) It must  be that 1 is
a key in a, and that key refers to either another associative array with a
1 key or a serial array with at least one element. (Maybe that's what you
mean by ambiguous.  That's true.)

Hope that helps.

Bob
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Re: [Jmol-developers] Alternative nested array element access syntax

[Robert Hanson]

see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.03.27.zip
​
:)
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[Jmol-developers] Fwd: JSmol php vulnerability

[Robert Hanson]

FYI
-- Forwarded message --
From: Robert Hanson hans...@stolaf.edu
Date: Mon, Mar 23, 2015 at 8:19 AM
Subject: JSmol php vulnerability
To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net


All developers are advised to replace on any server implementing JSmol

jsmol/php/jsmol.php

with

http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol_php

(with proper filename change back to jsmol.php), as it has a server
file-reading vulnerability.

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




-- 
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-developers] JSmol php vulnerability

[Robert Hanson]

The modified php file is part of Jmol 14.2 and 14.3 releases:

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.13/

https://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.13/



On Mon, Mar 23, 2015 at 8:19 AM, Robert Hanson hans...@stolaf.edu wrote:

 All developers are advised to replace on any server implementing JSmol

 jsmol/php/jsmol.php

 with

 http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol_php

 (with proper filename change back to jsmol.php), as it has a server
 file-reading vulnerability.

 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




-- 
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-developers] JSmol php vulnerability

[Robert Hanson]

However, SourceForge has not updated the default download yet nor made the
files available -- sorry, don't know why.

On Mon, Mar 23, 2015 at 10:03 AM, Robert Hanson hans...@stolaf.edu wrote:

 The modified php file is part of Jmol 14.2 and 14.3 releases:


 https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.13/


 https://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.13/



 On Mon, Mar 23, 2015 at 8:19 AM, Robert Hanson hans...@stolaf.edu wrote:

 All developers are advised to replace on any server implementing JSmol

 jsmol/php/jsmol.php

 with

 http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol_php

 (with proper filename change back to jsmol.php), as it has a server
 file-reading vulnerability.

 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




 --
 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




-- 
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-developers] Slow print command

[Robert Hanson]

I think you misunderstood, Rolf.

Right now

print

by itself throws an error.

I am proposing making that command -- by itself -- clear both the Jmol
console and the System.out JavaScript console (what is displayed using the
JSCONSOLE command).

So no loss to what we have; only a gain.

There is also an inconsistency I see with the JavaScript or Java applet,
but not the Java application, that

print 

also clears the Jmol console. I propose removing that and having it just
print a blank line, as is done for the application.

Bob


On Tue, Mar 10, 2015 at 11:42 AM, Rolf Huehne rhue...@fli-leibniz.de
wrote:

 On 03/10/2015 05:32 PM, Robert Hanson wrote:
  I could make
 
  print
 
 
  clear the console.
 
 That would be a very bad idea!

 Printing is done with a purpose. And for development and debugging it is
 really important to be able to see previous output and also the mixture
 of commands and the corresponding output.
 Clearing the console window should only be done manually!

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

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

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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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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.

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Re: [Jmol-developers] Slow print command

[Robert Hanson]

Try turning off the system console. Doesn't sound like you need it, and
that is probably what is slowing things down, not the Jmol console.

Info = {
...
  console: none,
...
}



On Wed, Mar 11, 2015 at 1:08 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 03/10/2015 10:07 PM, Robert Hanson wrote:
  that's a point.
  ​
  Take a look at the LOG command. If you are saving information, it
 probably
  makes more sense to put it into a file, not the console.
 
 Thank you for reminding me of it. For the application it solves my speed
 problem.
 But for the applet my coments still apply since 'log' doesn't work there
 according to the documentation.

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

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

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

 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228



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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-developers] Slow print command

[Robert Hanson]

Rolf,

I have not seen that issue -- I suppose this is going to the console, and
maybe your machine has memory issues with that -- too much printing? I did
recently set it to scroll to the end after each print, and that requires
calculating the number of characters, which I think Jmol perhaps was not
doing before. Check with a version that is a few months old and see if it
is the same or different, please.

Bob

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[Jmol-developers] list bounces

[Robert Hanson]

Who is handling these? Anyone?

jmol-users-boun...@lists.sourceforge.net

-- 
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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-developers] JSmol dipole bug?

[Robert Hanson]

Understood.

Jmol.zip at that site is not always the latest. I can be more diligent in
making it so, though.

This chemapps site is really for development only. I would not recommend
upgrading automatically from it. Sort of a nightly idea.
All the actual releases are at SourceForge.

Bob


On Tue, Jan 20, 2015 at 10:42 AM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 Btw. I've written an update script for my application which uses wget and
 unzip to update Jmol and JSmol. I'm using
 http://chemapps.stolaf.edu/jmol/zip/Jmol.zip but it looks like thats not
 the latest version according to the dates in
 http://chemapps.stolaf.edu/jmol/zip/. Is this only temporary? Or is there
 maybe another way to auto update Jmol? A zip is fine for me but there
 should be an official current release URL. Would it be possible to put it
 on GitHub? http://jmol.sourceforge.net/ seems a bit behind... If
 Jmol/JSmol does not use git, you should definitely use BitBucket. In GitHub
 you can do some pretty nice stuff with tags and releases.

 Op Tue Jan 20 2015 at 12:06:23 PM schreef Herman Bergwerf 
 hermanbergw...@gmail.com:

 Thank you! I will update Jmol ASAP

 Op Mon Jan 19 2015 at 23:53:48 schreef Robert Hanson hans...@stolaf.edu
 :

 Sorry about that!

 Jmol.___JmolVersion=14.3.11_2015.01.19


 bug fix: DIPOLE command broken in Jmol 14.3.10_2014.11.27 (OK in 14.2)


 releasing later today



 On Mon, Jan 19, 2015 at 1:32 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 select *; calculate partialcharge;
 dipole bonds on; dipole calculate bonds;

 This script is not working for me any more (no dipoles are drawn)
 I downloaded an old JSmol version (from may last year) and tested using
 this page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (but from
 the zip instead of course)
 Can you please fix this?

 
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 --
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 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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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-developers] JSmol dipole bug?

[Robert Hanson]

See http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.11_2015.01.20.zip

​This will read 2015.01.19 but its date should be today.

Jmol.___JmolVersion=14.3.11_2015.01.19

bug fix: Languages lost in Jmol Application
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Re: [Jmol-developers] JSmol dipole bug?

[Robert Hanson]

Actually, that just got updated. You will need that for your fix.

On Tue, Jan 20, 2015 at 1:04 PM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 I understand your point about the unstable zips. I added sourceforge to my
 update/build script (the newest version is just very tempting most of the
 time, especially after a bugfix) So I fetched the latest Jmol/JSmol version
 from SourgeFourge (14.2.9_2014.11.23) I think I will stick to sourgefourge
 for molview.org

 Op Tue Jan 20 2015 at 6:31:48 PM schreef Robert Hanson hans...@stolaf.edu
 :

 Understood.

 Jmol.zip at that site is not always the latest. I can be more diligent in
 making it so, though.

 This chemapps site is really for development only. I would not recommend
 upgrading automatically from it. Sort of a nightly idea.
 All the actual releases are at SourceForge.

 Bob


 On Tue, Jan 20, 2015 at 10:42 AM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 Btw. I've written an update script for my application which uses wget
 and unzip to update Jmol and JSmol. I'm using
 http://chemapps.stolaf.edu/jmol/zip/Jmol.zip but it looks like thats
 not the latest version according to the dates in
 http://chemapps.stolaf.edu/jmol/zip/. Is this only temporary? Or is
 there maybe another way to auto update Jmol? A zip is fine for me but there
 should be an official current release URL. Would it be possible to put it
 on GitHub? http://jmol.sourceforge.net/ seems a bit behind... If
 Jmol/JSmol does not use git, you should definitely use BitBucket. In GitHub
 you can do some pretty nice stuff with tags and releases.

 Op Tue Jan 20 2015 at 12:06:23 PM schreef Herman Bergwerf 
 hermanbergw...@gmail.com:

 Thank you! I will update Jmol ASAP

 Op Mon Jan 19 2015 at 23:53:48 schreef Robert Hanson 
 hans...@stolaf.edu:

 Sorry about that!

 Jmol.___JmolVersion=14.3.11_2015.01.19


 bug fix: DIPOLE command broken in Jmol 14.3.10_2014.11.27 (OK in 14.2)


 releasing later today



 On Mon, Jan 19, 2015 at 1:32 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 select *; calculate partialcharge;
 dipole bonds on; dipole calculate bonds;

 This script is not working for me any more (no dipoles are drawn)
 I downloaded an old JSmol version (from may last year) and tested
 using this page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 (but from the zip instead of course)
 Can you please fix this?

 
 --
 New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
 GigeNET is offering a free month of service with a new server in
 Ashburn.
 Choose from 2 high performing configs, both with 100TB of bandwidth.
 Higher redundancy.Lower latency.Increased capacity.Completely
 compliant.
 http://p.sf.net/sfu/gigenet
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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

  
 --
 New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
 GigeNET is offering a free month of service with a new server in
 Ashburn.
 Choose from 2 high performing configs, both with 100TB of bandwidth.
 Higher redundancy.Lower latency.Increased capacity.Completely
 compliant.
 http://p.sf.net/sfu/gigenet_
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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

  
 --
 New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
 GigeNET is offering a free month of service

Re: [Jmol-developers] JSmol dipole bug?

[Robert Hanson]

Sorry about that!

Jmol.___JmolVersion=14.3.11_2015.01.19


bug fix: DIPOLE command broken in Jmol 14.3.10_2014.11.27 (OK in 14.2)


releasing later today



On Mon, Jan 19, 2015 at 1:32 PM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 select *; calculate partialcharge;
 dipole bonds on; dipole calculate bonds;

 This script is not working for me any more (no dipoles are drawn)
 I downloaded an old JSmol version (from may last year) and tested using
 this page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (but from the
 zip instead of course)
 Can you please fix this?


 --
 New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
 GigeNET is offering a free month of service with a new server in Ashburn.
 Choose from 2 high performing configs, both with 100TB of bandwidth.
 Higher redundancy.Lower latency.Increased capacity.Completely compliant.
 http://p.sf.net/sfu/gigenet
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




-- 
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
--
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet___
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Re: [Jmol-developers] Mysterious behaviour of JavaScript 'for' loops after initializing JSmol

[Robert Hanson]

I guess JSmol is incompatible with certain uses of String. In particular,
when JSmol is initialized,

x.toString()

becomes a String Object, not just a simple string, as it must. There is
no way around that.

jqGrid in one place then uses the strictly equals === to compare the
desired row id to the id attribute of a table row:

if( rowid.toString() === this.rows[i].id) {...}

Well, that won't work now, because rowid.toString() is an object, and
this.rows[i].id is a string.

The use of === is unnecessary here. A table row attribute is guaranteed to
be a string, and so is x.toString().
So == is sufficient. It's just a bit of overkill on the part of the jqGrid
developers.

I'm not sure why it is specific to Chrome.

Bob




On Fri, Jan 16, 2015 at 5:27 AM, Markus Wiederstein mar...@came.sbg.ac.at
wrote:

 Hi developers,

 we recently noticed a curious effect of JSmol initialization on looping
 over an array in JavaScript: it seems that the construct 'for (var i in
 data)' does not work in the expected way anymore after JSmol
 initialization.  More precisely, the loop is not only over the keys of the
 array but also includes apparent methods of the array(?) object.

 Here's a small test page that illustrates this behaviour:

 http://topsearch.services.came.sbg.ac.at/jsmol_bug_mini.html

 The nasty thing about this is that it seems to prevent JSmol to work
 properly with jqGrid in Chromium (see 3. in test page).

 We are currently stuck in trying to find out what's going on here...

 Any help is greatly appreciated,
 with best regards,

 -Markus


 --
 Dr. Markus Wiederstein, Assoc. Prof.
 University of Salzburg
 Department of Molecular Biology
 Division of Bioinformatics /
 Center of Applied Molecular Engineering
 Hellbrunnerstr. 34
 A-5020 Salzburg
 Tel: +43 662 8044 5794


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 GigeNET is offering a free month of service with a new server in Ashburn.
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-- 
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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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GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
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Re: [Jmol-developers] Mysterious behaviour of JavaScript 'for' loops after initializing JSmol

[Robert Hanson]

(so go into jqGrid and change that === to == )

​
--
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GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
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Re: [Jmol-developers] Mysterious behaviour of JavaScript 'for' loops after initializing JSmol

[Robert Hanson]

Here's the exact difference before and after loading JSmol in Firefox and
Chrome:

Firefox:

new String(test).toString() === test
[JSmol initializes]
new String(test).toString() === test


new String(test).toString() === test
[JSmol initializes]
new String(test).toString() !== test

I found the bug in JSmol. In the mean time, if you want to check this,
please replace in j2s/core/core.z.js:

String.prototype.toString=function(){return this}

with

String.prototype.toString=function(){return this.valueOf()}


Please let me know if that fixes the problem.







On Fri, Jan 16, 2015 at 9:04 AM, Robert Hanson hans...@stolaf.edu wrote:

 (so go into jqGrid and change that === to == )

 ​




-- 
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
--
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet___
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Re: [Jmol-developers] setAppletCss

[Robert Hanson]

thanks -- found it.

On Sat, Dec 6, 2014 at 6:37 AM, Angel Herráez angel.herr...@uah.es wrote:

 It seems that setAppletCss() is not working, tested in JSmol 14.3.10

 Case example: the button has red border, but the JSmol object has not:

 head
 style type=text/css
 .grayBox { border:1px solid red; }
 /style
 /head

 body
 script type=text/javascript
 Jmol.setAppletCss('grayBox');
 Jmol.setButtonCss('grayBox');
 Jmol.getApplet('myJmol', Info);
 Jmol.jmolButton(myJmol, ' ', 'test')
 /script
 /body



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-- 
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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-developers] Customized application menu

[Robert Hanson]

[I prefer to refer to the Java application as Jmol still, not JSmol,
please. That's too twisted for me!]




On Wed, Dec 3, 2014 at 6:48 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:

Hi developers,

 I would like to know if it would be possible to make the JSmol
 application main menu customizable on the fly (like the popup menu) and
 ideally also the icon toolbar with customized icons?


not possible. These are hard-coded


 Since 'Java webstart' supposedly will be the only alternative to get the
 Java version of JSmol running from the Web after (some of) the major
 browsers have dropped the Java plugins, it would be helpful to have also
 more control over the appearance and functionality of the application.



That's not entirely true. You can run the Jmol Java applet outside a
browser. Just start the JNLP files in the java directory of the JSmol
distribution. That's entirely outside any browser.




 Another use case for a customizable application would be if someone
 (like me) would like to use the JSmol application with a different focus
 than molecular structures or enhance for example the modelkit
 functionality or the application functionality in general.


I do think this is an interesting suggestion. What about the Macros menu?
This seems to be under-utilized.

Bob
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Re: [Jmol-developers] Customized application menu

[Robert Hanson]

On Wed, Dec 3, 2014 at 9:19 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 12/03/2014 02:00 PM, Robert Hanson wrote:
  [I prefer to refer to the Java application as Jmol still, not JSmol,
  please. That's too twisted for me!]
 
 Bob, but wasn't it you who turned away from the separation at the
 beginning into JSmol=Javascript and Jmol=Java to
 JSmol=Javascript/Java/WebGL making everything to JSmol, logically also
 including the application?
 To avoid confusions I just have adapted to that and started to think of
 Jmol as JSmol in general.


I make the distinction for the Java application still.


  application main menu customizable on the fly (like the popup menu) and
  ideally also the icon toolbar with customized icons?
 
 
  not possible. These are hard-coded
 
 So to change anything in the toolbar or the main menu even only at
 startup it would be necessary to build a seperate other application?


well, or rewrite some code to load auxiliary files or something like that.


 
  Since 'Java webstart' supposedly will be the only alternative to get the
  Java version of JSmol running from the Web after (some of) the major
  browsers have dropped the Java plugins, it would be helpful to have also
  more control over the appearance and functionality of the application.
 
 
 
  That's not entirely true. You can run the Jmol Java applet outside a
  browser. Just start the JNLP files in the java directory of the JSmol
  distribution. That's entirely outside any browser.
 
 The applet would be fully functional except for stuff related to browser
 communication?


right -- just no JavaScript buttons and such -- the frame itself only



 Could the Java console also be opened like in the application?


The Jmol applet console opens in a separate frame in front of the applet.


 
 
 
  Another use case for a customizable application would be if someone
  (like me) would like to use the JSmol application with a different focus
  than molecular structures or enhance for example the modelkit
  functionality or the application functionality in general.
 
 
  I do think this is an interesting suggestion. What about the Macros menu?
  This seems to be under-utilized.
 
 For enhancements this could be useful. But for shifting the focus it
 would be necessary to get rid and/or rename some of the existing menu
 entries or toolbar icons.


If there's much to change, that's certainly writing a new application. You
need a whole raft of additional files -- icons, button layouts, all sorts
of things. The top application menu is basically a text file that could be
read on demand. See
sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/Properties/Jmol-resources.properties

A good project for a volunteer, perhaps. Not I.





 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
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-- 
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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-developers] Bug in JSmol-JSme integration

[Robert Hanson]

this is fixed http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.10.12.zip

On Tue, Sep 9, 2014 at 7:07 AM, Robert Hanson hans...@stolaf.edu wrote:

 I noticed that. Thanks for pointing it out. Let me know if you figure out
 what is happening there.

 On Tue, Sep 9, 2014 at 12:49 AM, Johannes | edumol.fi edu...@edumol.fi
 wrote:

  New bug in the latest release:
 http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm

 If I search a new molecule on the 2D-side, it wont't update it to the
 3D-side.

 jsmetest2.html http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
 works correctly.




 On 8.9.2014 15:53, edu...@edumol.fi wrote:

 Hello Bob.

 Both links that you sent are working correctly. Excellent!

 The zip-package from this morning seemed to contain version 14.3.6 (
 http://edumol.fi/dev/jsmol-14.3.7_2014.09.07c/jsmol/jsmetest.htm) and
 the link where it is working has a number 14.3.7.

 Thank you.

 Johannes



 Robert Hanson kirjoitti 08.09.2014 15:34:

  I see still a different problem at
 http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm

  Am I correct that it is working correctly at

 http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
 ?

 ​

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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




-- 
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-developers] JSmol as network viewer

[Robert Hanson]

On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:

Hi developers,


 Q: I was wondering if it might be possible to achieve this by tuning the
 'minimize' command with some extra parameters or maybe by enabling to
 define a custom 'minimize' function?


I think if you did UFF minimization you could adapt
j2s/J/minimize/forcefield/data/UFF.txt to just about anything you wanted to.




 Regards,
 Rolf
 --

 Rolf Huehne
 Postdoc

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

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

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

 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228



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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-developers] JSmol as network viewer

[Robert Hanson]

Probably not. I didn't realize we were talking about quite so many nodes.
Still, the UFF field is interesting because it might work with any geometry
-- leaving angles out all together. We might have to add something to get
it to ignore certain energy components. Angles and dihedrals, for instance.

On Mon, Oct 6, 2014 at 9:55 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:

 On 10/06/2014 02:22 PM, Robert Hanson wrote:
  On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de
 wrote:
 
  Hi developers,
 
 
  Q: I was wondering if it might be possible to achieve this by tuning the
  'minimize' command with some extra parameters or maybe by enabling to
  define a custom 'minimize' function?
 
 
  I think if you did UFF minimization you could adapt
  j2s/J/minimize/forcefield/data/UFF.txt to just about anything you wanted
 to.
 
 Bob, do you really think that it will be possible to adapt the
 parameters in the UFF file to cope with atoms that can have several
 hundred or even thousands of bonds and get a reasonable network layout?
 At a first glance it doesn't look very likely for me. But I must admit
 that I have never dealt with UFF or something similar before.

 Regards,
 Rolf

 --

 Rolf Huehne
 Postdoc

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

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

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

 VAT No: DE 153 925 464
 Register of Associations: No. 230296, Amtsgericht Jena
 Tax Number: 162/141/08228



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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-developers] java to javascript conversion

[Robert Hanson]

Kent, this is not an easy thing at all to describe. Basically a lot of
customization was done. I have now converted two other programs (JSpecView
and AztexViewer)  The first took *me* a month, and the second took 10 days.
So I am getting better at it, but it is no simple task to describe how it
is done. If you have any GUI, it's probably not possible at this point.
I've got that somewhat set up, but it is quite primitive.

Bob


On Sun, Sep 28, 2014 at 12:57 PM, R. Kent Wenger wen...@cs.wisc.edu wrote:

 I maintain some software for the BioMagResBank (http://www.bmrb.wisc.edu/)
 that's written in Java and incorporates Jmol.  Because of the recent
 issues with Java security, we're investigating converting the whole thing
 to JavaScript.  Hopefully we can use JSmol as a pretty direct substitute
 for Jmol, but we have quite a bit of our own Java code to convert.

 We're hoping that we can do at least a good chunk of the conversion with
 java2js, but I haven't had much luck with that tool so far.  I downloaded
 and installed apache cxf, but when I run java2js I *always* get this
 error:

 JavaToJS Error :
 org.apache.cxf.tools.common.toolspec.parser.BadUsageException: Missing
 argument: classname

 As I recall at least some of the Jmol to JSmol conversion was done with
 java2js -- I'm hoping that someone on this list can point me at least a
 little bit in the right direction in getting java2js to work...

 An actual example of using java2js, even on super-simple Java code, would
 be really helpful.

 Kent
 --
 R. Kent Wenger (wen...@cs.wisc.edu, 608-262-6627,
 http://www.cs.wisc.edu/~wenger/)
 Computer Sciences Department
 University of Wisconsin-Madison


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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.

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Re: [Jmol-developers] chainCaseSensitive is forced true in 14.3.7

[Robert Hanson]

I would appreciate thoughts on this:

There was a bug in the chain case sensitivity that forced select :a to
not match A in a PDB file chain designation, and that is fixed, but
besides that there is an issue for which all should be aware and for which
I would like your thoughts.

Nine years ago Miguel introduced

  set chainCaseSensitive (default FALSE)

[http://ehc.ac/p/jmol/mailman/message/10315720/]

That was then. Now we have multiple-character chains and lots of overflow
from upper case A-Z to lower-case a-z in PDB chain designations. I am
trying to create an algorithm that respects old situations and still
doesn't require this special flag for new structures that are starting to
have lower-case letters for chains (1S5L, 1VSP, others?).

My idea is this:

(1) If files loaded have no lower-case chain labels and all are
single-character, match them as always, based on the setting of
chainCaseSensitive; default for which is FALSE:

load =1d66
select :a
468 atoms selected
select :A
468 atoms selected

The idea is that the original idea of chainCaseSensitive was to allow :a
to match A in a PDB file, not so much to allow :A to match a in the
PDB file.

Correct?

(2) If any one of the current files loaded has lower-case chain characters
or multi-character chains, then it seems to me Jmol should disregard the
setting of chainCaseSensitive and just consider its value to be TRUE. This
is because if there really is a lower-case chain, then why NOT be
case-sensitive? Surely it means there are A and a, and those are totally
different chains. And if there are multi-character chains, then we are in a
new world, and we should respect those letter cases and just say it's case
sensitive for them.

Thus:

(1) When any currently loaded files have lower-case or multi-letter chain
identifiers
 -- chainCaseSensitive ignored

(2) When all currently loaded files have non-alphabetic or only upper-case
chain identifiers
 -- chainCaseSensitive respected


Bob





On Tue, Sep 9, 2014 at 12:11 PM, Angel Herráez angel.herr...@uah.es wrote:

 There is also a problem with numeric chain IDs:

 load =1LMB;

 select *:1;   //selects chains 1 and 2
 select *:2;   // same atoms

 select *:3;   //selects chains 3 and 4
 select *:4;   // same atoms

 I notice that hover display quotes around the ID, like

 [DG]37:2.O3'

 so I tried
 select *:1
 without change




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


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Re: [Jmol-developers] cartoon for Calpha-only is broken

[Robert Hanson]

Right - I forgot to do a full clean before creating the JAR file. Oh, I
hate that bug in Eclipse

Will update again now.



On Mon, Sep 15, 2014 at 8:52 AM, Angel Herráez angel.herr...@uah.es wrote:

 9 Sep 2014, 2:58, Robert Hanson wrote:
  In addition to that, the chain read from then HELIX record was not
  stored the same way, so helixes and sheets were not read for any
  chain that was outside the range A - Z.


 Partly solved, but with another glitch now present:

  in 14.3.7_2014.09.08b
  load =1LMB
  cartoon only  // ok for dna, not for protein

 in 14.3.7_2014.09.14
 load =1LMB
 cartoon only  // ok for protein, nothing is displayed  for DNA



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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-developers] cartoon for Calpha-only is broken

[Robert Hanson]

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.15b.zip

On Mon, Sep 15, 2014 at 9:58 AM, Robert Hanson hans...@stolaf.edu wrote:

 Right - I forgot to do a full clean before creating the JAR file. Oh, I
 hate that bug in Eclipse

 Will update again now.



 On Mon, Sep 15, 2014 at 8:52 AM, Angel Herráez angel.herr...@uah.es
 wrote:

 9 Sep 2014, 2:58, Robert Hanson wrote:
  In addition to that, the chain read from then HELIX record was not
  stored the same way, so helixes and sheets were not read for any
  chain that was outside the range A - Z.


 Partly solved, but with another glitch now present:

  in 14.3.7_2014.09.08b
  load =1LMB
  cartoon only  // ok for dna, not for protein

 in 14.3.7_2014.09.14
 load =1LMB
 cartoon only  // ok for protein, nothing is displayed  for DNA



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 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




-- 
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-developers] Measurement bug?

[Robert Hanson]

(right mouse button menu  Measurements  ...)

is the hint I needed. Very nice fix. I like this feel much better!

http://chemapps.stolaf.edu/jmo/zip/jmol-14.3.7_2014.09.10.zip

Jmol.___JmolVersion=14.3.7_2014.09.10

bug fix: Pending measurements lost when dragging to reposition molecule



On Wed, Sep 10, 2014 at 3:24 AM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 I get it. The designed behavior would be OK but the problem/bug is as you
 described secondly (for me at least)
 I could listen to the messagecallback and fully terminate the pending
 measurement from there (if the dismiss is reported there)
 On Sep 9, 2014 10:19 PM, Robert Hanson hans...@stolaf.edu wrote:

 The normal, designed response is that any dragging of the model during a
 measurement terminates the pending measurement. You must start again. If
 that is all the problem is, then that's by design.

 If the problem is that you lose some control over a pending measurement
 but it continues to be in effect, then that's a bug.


 On Tue, Sep 9, 2014 at 1:17 PM, Herman Bergwerf hermanbergw...@gmail.com
  wrote:

 It has nothing to do with keys. Just hold a mousebutton and drag (the
 dotted line should disappear when you drag)

 You can also use:
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 (right mouse button menu  Measurements  ...)

 Real world example:
 You start an angle measurement.
 You want to rotate the molecule in order to click the 3rd atom
 Try to rotate the model while performing the measurement
 (I would expect the dotted line to re-appear after I've rotated the
 model)

 2014-09-09 20:00 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 I can't reproduce the issue. Thought I could, but now I can't. Possibly
 had something to do with whether I was holding keys down after clicking
 (press+release) or just pressing.

 On Tue, Sep 9, 2014 at 9:24 AM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 You mean you can't reproduce the issue?

 2014-09-09 1:17 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 Nope, I thought  I had it, but I can't do it now. What's the trick?

 On Mon, Sep 8, 2014 at 6:03 PM, Robert Hanson hans...@stolaf.edu
 wrote:

 sure, I see. I can fix that...

 On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 I can't find a way to reproduce the exact issue but I can reproduce
 the behaviour:

 goto http://molview.org
 click Jmol  Measurement  Torsion (4 atoms)
 click 1st atom
 click 2nd atom AND HOLD + DRAG
 try to finish your measurement (works sometimes but pre-dotted line
 is gone)

 I'm not sure if there is something else causing this issue too or
 I'm dragging the pointer ~1px every time this happens.

 I let you know if I find a better method.

 2014-09-08 21:25 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 This is news to me. See if you can describe a reproducible way of
 generating the problem.

 On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 This is actually an old bug but I was wondering if it is possible
 to fix it.
 When I perform a measurement, sometimes the pre-dotted line
 disappears and I can't start the measurement over again (it's still 
 in
 'progress' but kind of broken because you can't just finish the 
 'invisible'
 measurement by clicking an atom)
 Does anyone recognize this behaviour?
 It would be great if this can be improved/patched (a hover style
 for an atom would also be very cool)

 Thanks!
 Herman


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 Robert M. Hanson
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 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-developers] Bug in JSmol-JSme integration

[Robert Hanson]

I noticed that. Thanks for pointing it out. Let me know if you figure out
what is happening there.

On Tue, Sep 9, 2014 at 12:49 AM, Johannes | edumol.fi edu...@edumol.fi
wrote:

  New bug in the latest release:
 http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm

 If I search a new molecule on the 2D-side, it wont't update it to the
 3D-side.

 jsmetest2.html http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
 works correctly.




 On 8.9.2014 15:53, edu...@edumol.fi wrote:

 Hello Bob.

 Both links that you sent are working correctly. Excellent!

 The zip-package from this morning seemed to contain version 14.3.6 (
 http://edumol.fi/dev/jsmol-14.3.7_2014.09.07c/jsmol/jsmetest.htm) and the
 link where it is working has a number 14.3.7.

 Thank you.

 Johannes



 Robert Hanson kirjoitti 08.09.2014 15:34:

  I see still a different problem at
 http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm

  Am I correct that it is working correctly at

 http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
 ?

 ​

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-- 
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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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Manually upgrade your production database.
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Re: [Jmol-developers] cartoon for Calpha-only is broken

[Robert Hanson]

This relates to the chain case issue as well. Jmol is set to force case
sensitivity if it finds (a) chain designations of more than one character
or (b) ones with lower case. Unfortunately, it was considering 1 to be
lower case.

In addition to that, the chain read from then HELIX record was not stored
the same way, so helixes and sheets were not read for any chain that was
outside the range A - Z.

Bob


On Tue, Sep 9, 2014 at 12:26 PM, Angel Herráez angel.herr...@uah.es wrote:

 sorry, that's not Calpha-only

 But the problem is present --now I don't know the reason





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-- 
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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
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce.
Perforce version control. Predictably reliable.
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Re: [Jmol-developers] Measurement bug?

[Robert Hanson]

I can't reproduce the issue. Thought I could, but now I can't. Possibly had
something to do with whether I was holding keys down after clicking
(press+release) or just pressing.

On Tue, Sep 9, 2014 at 9:24 AM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 You mean you can't reproduce the issue?

 2014-09-09 1:17 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 Nope, I thought  I had it, but I can't do it now. What's the trick?

 On Mon, Sep 8, 2014 at 6:03 PM, Robert Hanson hans...@stolaf.edu wrote:

 sure, I see. I can fix that...

 On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 I can't find a way to reproduce the exact issue but I can reproduce
 the behaviour:

 goto http://molview.org
 click Jmol  Measurement  Torsion (4 atoms)
 click 1st atom
 click 2nd atom AND HOLD + DRAG
 try to finish your measurement (works sometimes but pre-dotted line is
 gone)

 I'm not sure if there is something else causing this issue too or I'm
 dragging the pointer ~1px every time this happens.

 I let you know if I find a better method.

 2014-09-08 21:25 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 This is news to me. See if you can describe a reproducible way of
 generating the problem.

 On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 This is actually an old bug but I was wondering if it is possible to
 fix it.
 When I perform a measurement, sometimes the pre-dotted line
 disappears and I can't start the measurement over again (it's still in
 'progress' but kind of broken because you can't just finish the 
 'invisible'
 measurement by clicking an atom)
 Does anyone recognize this behaviour?
 It would be great if this can be improved/patched (a hover style for
 an atom would also be very cool)

 Thanks!
 Herman


 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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



 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
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 --
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 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

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 ___
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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




 --
 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



 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce.
 Perforce version control. Predictably

Re: [Jmol-developers] Measurement bug?

[Robert Hanson]

The normal, designed response is that any dragging of the model during a
measurement terminates the pending measurement. You must start again. If
that is all the problem is, then that's by design.

If the problem is that you lose some control over a pending measurement but
it continues to be in effect, then that's a bug.


On Tue, Sep 9, 2014 at 1:17 PM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 It has nothing to do with keys. Just hold a mousebutton and drag (the
 dotted line should disappear when you drag)

 You can also use:
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
 (right mouse button menu  Measurements  ...)

 Real world example:
 You start an angle measurement.
 You want to rotate the molecule in order to click the 3rd atom
 Try to rotate the model while performing the measurement
 (I would expect the dotted line to re-appear after I've rotated the model)

 2014-09-09 20:00 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 I can't reproduce the issue. Thought I could, but now I can't. Possibly
 had something to do with whether I was holding keys down after clicking
 (press+release) or just pressing.

 On Tue, Sep 9, 2014 at 9:24 AM, Herman Bergwerf hermanbergw...@gmail.com
  wrote:

 You mean you can't reproduce the issue?

 2014-09-09 1:17 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 Nope, I thought  I had it, but I can't do it now. What's the trick?

 On Mon, Sep 8, 2014 at 6:03 PM, Robert Hanson hans...@stolaf.edu
 wrote:

 sure, I see. I can fix that...

 On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 I can't find a way to reproduce the exact issue but I can reproduce
 the behaviour:

 goto http://molview.org
 click Jmol  Measurement  Torsion (4 atoms)
 click 1st atom
 click 2nd atom AND HOLD + DRAG
 try to finish your measurement (works sometimes but pre-dotted line
 is gone)

 I'm not sure if there is something else causing this issue too or I'm
 dragging the pointer ~1px every time this happens.

 I let you know if I find a better method.

 2014-09-08 21:25 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 This is news to me. See if you can describe a reproducible way of
 generating the problem.

 On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 This is actually an old bug but I was wondering if it is possible
 to fix it.
 When I perform a measurement, sometimes the pre-dotted line
 disappears and I can't start the measurement over again (it's still in
 'progress' but kind of broken because you can't just finish the 
 'invisible'
 measurement by clicking an atom)
 Does anyone recognize this behaviour?
 It would be great if this can be improved/patched (a hover style
 for an atom would also be very cool)

 Thanks!
 Herman


 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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



 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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




 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Department

Re: [Jmol-developers] Bug in JSmol-JSme integration

[Robert Hanson]

I see still a different problem at
http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm

Am I correct that it is working correctly at

http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
?

​
--
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Re: [Jmol-developers] Measurement bug?

[Robert Hanson]

This is news to me. See if you can describe a reproducible way of
generating the problem.

On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 This is actually an old bug but I was wondering if it is possible to fix
 it.
 When I perform a measurement, sometimes the pre-dotted line disappears and
 I can't start the measurement over again (it's still in 'progress' but kind
 of broken because you can't just finish the 'invisible' measurement by
 clicking an atom)
 Does anyone recognize this behaviour?
 It would be great if this can be improved/patched (a hover style for an
 atom would also be very cool)

 Thanks!
 Herman


 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




-- 
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
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Measurement bug?

[Robert Hanson]

sure, I see. I can fix that...

On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 I can't find a way to reproduce the exact issue but I can reproduce the
 behaviour:

 goto http://molview.org
 click Jmol  Measurement  Torsion (4 atoms)
 click 1st atom
 click 2nd atom AND HOLD + DRAG
 try to finish your measurement (works sometimes but pre-dotted line is
 gone)

 I'm not sure if there is something else causing this issue too or I'm
 dragging the pointer ~1px every time this happens.

 I let you know if I find a better method.

 2014-09-08 21:25 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 This is news to me. See if you can describe a reproducible way of
 generating the problem.

 On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf hermanbergw...@gmail.com
  wrote:

 This is actually an old bug but I was wondering if it is possible to fix
 it.
 When I perform a measurement, sometimes the pre-dotted line disappears
 and I can't start the measurement over again (it's still in 'progress' but
 kind of broken because you can't just finish the 'invisible' measurement by
 clicking an atom)
 Does anyone recognize this behaviour?
 It would be great if this can be improved/patched (a hover style for an
 atom would also be very cool)

 Thanks!
 Herman


 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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



 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




-- 
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
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Measurement bug?

[Robert Hanson]

Nope, I thought  I had it, but I can't do it now. What's the trick?

On Mon, Sep 8, 2014 at 6:03 PM, Robert Hanson hans...@stolaf.edu wrote:

 sure, I see. I can fix that...

 On Mon, Sep 8, 2014 at 2:36 PM, Herman Bergwerf hermanbergw...@gmail.com
 wrote:

 I can't find a way to reproduce the exact issue but I can reproduce the
 behaviour:

 goto http://molview.org
 click Jmol  Measurement  Torsion (4 atoms)
 click 1st atom
 click 2nd atom AND HOLD + DRAG
 try to finish your measurement (works sometimes but pre-dotted line is
 gone)

 I'm not sure if there is something else causing this issue too or I'm
 dragging the pointer ~1px every time this happens.

 I let you know if I find a better method.

 2014-09-08 21:25 GMT+02:00 Robert Hanson hans...@stolaf.edu:

 This is news to me. See if you can describe a reproducible way of
 generating the problem.

 On Mon, Sep 8, 2014 at 1:57 PM, Herman Bergwerf 
 hermanbergw...@gmail.com wrote:

 This is actually an old bug but I was wondering if it is possible to
 fix it.
 When I perform a measurement, sometimes the pre-dotted line disappears
 and I can't start the measurement over again (it's still in 'progress' but
 kind of broken because you can't just finish the 'invisible' measurement by
 clicking an atom)
 Does anyone recognize this behaviour?
 It would be great if this can be improved/patched (a hover style for an
 atom would also be very cool)

 Thanks!
 Herman


 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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



 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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




-- 
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
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Jmol.resizeApplet

[Robert Hanson]

only the latter [w,h], I think.

On Sat, Sep 6, 2014 at 6:27 PM, Angel Herráez angel.herr...@uah.es wrote:

 Bob, are both syntaxes supported?

 Jmol.resizeApplet(appletid, w, h)

 Jmol.resizeApplet(appletid, [w,h])

 I only had the 2nd documented
 http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#resizeApple
 t




 --
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 ___
 Jmol-developers mailing list
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 https://lists.sourceforge.net/lists/listinfo/jmol-developers




-- 
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
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___
Jmol-developers mailing list
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https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Jmol.resizeApplet

[Robert Hanson]

If you have two applets, you need to be sure they have different names.
That could cause this sort of thing.

On Sun, Sep 7, 2014 at 9:04 PM, Robert Hanson hans...@stolaf.edu wrote:

 only the latter [w,h], I think.

 On Sat, Sep 6, 2014 at 6:27 PM, Angel Herráez angel.herr...@uah.es
 wrote:

 Bob, are both syntaxes supported?

 Jmol.resizeApplet(appletid, w, h)

 Jmol.resizeApplet(appletid, [w,h])

 I only had the 2nd documented

 http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#resizeApple
 t




 --
 Slashdot TV.
 Video for Nerds.  Stuff that matters.
 http://tv.slashdot.org/
 ___
 Jmol-developers mailing list
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 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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




-- 
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
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Bug in JSmol-JSme integration

[Robert Hanson]

I believe I have that fixed. Check the latest zip file:

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.07b.zip

(uploading now)

​
--
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When you want reliability, choose Perforce
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Re: [Jmol-developers] Jmol.resizeApplet

[Robert Hanson]

I think I found it. It will be part of 14.3.7 and 14.2.7, probably later
this weekend.


On Sat, Sep 6, 2014 at 5:14 PM, Herman Bergwerf hermanbergw...@gmail.com
wrote:

 On my tablet, Jmol.resizeApplet(JSmol, [w,h]) creates a new canvas insead
 of resizing the existing canvas causing JSmol to become useless.
 The console also told me this:
 Uncaught TypeError: Cannot read property 'processTwoPointGesture' of
 undefined

 Strangely, everything is alright in the current stable version of my
 application: http://molview.org which uses a slightly older version of
 JSmol.


 --
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 ___
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 https://lists.sourceforge.net/lists/listinfo/jmol-developers




-- 
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
--
Slashdot TV.  
Video for Nerds.  Stuff that matters.
http://tv.slashdot.org/___
Jmol-developers mailing list
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https://lists.sourceforge.net/lists/listinfo/jmol-developers

Re: [Jmol-developers] Jmol.resizeApplet

[Robert Hanson]

Sorry - that was in response to your other message, about multitouch.

I am not seeing any issue with Jmol.resizeApplet(appletid, width, height)

Looks to me like you do not have an applet with id JSmol.

These are two unrelated issues, right?




On Sat, Sep 6, 2014 at 5:51 PM, Robert Hanson hans...@stolaf.edu wrote:

 I think I found it. It will be part of 14.3.7 and 14.2.7, probably later
 this weekend.


 On Sat, Sep 6, 2014 at 5:14 PM, Herman Bergwerf hermanbergw...@gmail.com
 wrote:

 On my tablet, Jmol.resizeApplet(JSmol, [w,h]) creates a new canvas insead
 of resizing the existing canvas causing JSmol to become useless.
 The console also told me this:
 Uncaught TypeError: Cannot read property 'processTwoPointGesture' of
 undefined

 Strangely, everything is alright in the current stable version of my
 application: http://molview.org which uses a slightly older version of
 JSmol.


 --
 Slashdot TV.
 Video for Nerds.  Stuff that matters.
 http://tv.slashdot.org/
 ___
 Jmol-developers mailing list
 Jmol-developers@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-developers




 --
 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




-- 
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-developers] how to modify circle color of element node

[Robert Hanson]

Unless you are doing very major changes, there is no need to modify
classes. Just be sure you are operating on the trunk code and you keep it
up to date.


On Fri, Aug 15, 2014 at 7:36 PM, 胡瑞 huruid...@gmail.com wrote:

 OH I will not change anything on your original source code, but firstly, i
 need test and understand jmol runing way, if i will start modify offically
 i will extend your Class, modify original code is really bad way :(
 Sir i am a new programmer, i don't know how to read your svn file, Could
 you give me some advice
 Thank you very much


 2014-08-16 8:15 GMT+08:00 Robert Hanson hans...@stolaf.edu:

 ps -- make sure you are checking out
 svn.code.sf.net/p/jmol/code/trunk/Jmol


 On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu
 wrote:

 It sounds like you are a new contributor to Jmol. Terrific! We could use
 someone who wants to make the Gaussian input dialog better. No one has
 worked on that for a long time. Before you go too far on your own, though,
 why not request features? It would be unwise to start changing the code in
 Viewer, especially, because I regularly work on that, and what I do may
 break what you do. And you may not think of the implications something has,
 the way I can if I help you.

 I just checked in a much more interesting Gaussian input dialog. I hope
 you like it.

 Note that:

  -- tabs are gone; advanced simply right side of a JSplitPane
  -- refresh button is new; cancel button is now close
  -- when you use the model kit to modify the structure, the input file
 is updated
  -- when you click on an atom, that atom is selected and highlighted on
 the input file
  -- when you click on a line in the input file, the atom is highlighted
  -- when you change input parameters, the input file is updated
  -- when you load a new model, the input file is updated

 Bob


 On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote:

 Oh, sir I find there is a assignAtom function which allocate in the
 ModelSet Class(Figure 1)
 i fund two method will call this function, as i say in the photo there
 are all in the script package, but i just click gui and i don't input any
 script command. Am i going a right way ?


 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com:

 Thank you sir, i had saw those documents which use by script, That
 script just show me how to operate it. However, i need to modify jmol java
 source code and add a new function, i have a simple demo (Figure1). That
 function will provide many possible options to user to choice.  But how to
 recored user choice? Recoding index of element is very important.I still
 can't find the core function in the jmol opensource,Could you tell me the
 point of package and core class?
 Jmol sourse code is a huge project, i spend one month on this
 opensource code, many of them i can understand , some of them look so
 complicated.



 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu:

  Dear 胡瑞

 see below

 [translation]
 It is great to know that you have a Chinese team [to understand my
 point in Chinese]. Maybe I had not expressed myself well. I am student at
 University of New Haven, and my supervisor has asked me to add a new
 functionality on top of Jmol. Did you remember that Jmol has a menu item
 for Export Gaussian Input file? The advance option can record the 
 data
 on display. When I add element at the main menu, I must first switch [to
 the submenu?] to change options in advance. When I add a new structure,
 my results are sorted in order by default (see Figure 1, where the 2nd C
 should be at the 5th position) . How do I get the data in original order?

 The second question is how to record which element is clicked by a
 user. This info is useful to restore to the previous state. I am not
 familiar with scripting languages. However, browsing the source code 
 shows
 me that many functionalities are achieved by filtering strings, which is
 quite general strategy. I wish your team could provide a detailed
 documentation. There is very limit such info on the Internet. I need to
 know in detail the functionality of each class.
 [/translation]

 Order: There is no order sorting. The order is file order. But I see
 what you mean. There is a bug there, and I will look into it. I like the
 idea very much of being able to edit the model and see changes in the
 Gaussian advanced tab. Is that what you are interested in?  I have never
 thought of doing that.

 Documentation for scripting is at
 http://chemapps.stolaf.edu/jmol/docs  There is probably no need to
 do any actual Java programming -- you can do a lot with Jmol scripting. 
 For
 example, you can run your own functions whenever atoms are clicked. Look 
 up
 information on callbacks
 http://chemapps.stolaf.edu/jmol/docs/?search=callback

 No promises I can continue in Chinese -- do try English! :)

 Bob Hanson