Re: [Jmol-users] (no subject)

[Otis Rothenberger]

Interesting.

That’s the JME Editor in the app. I don’t have an Android device, but from the 
developer photos, it’s JME.

Otis
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> On Aug 25, 2016, at 8:14 AM, pinostricc...@alice.it wrote:
> 
> Dear Friends, has any of you had the chance to use the app on android called 
> Mo-Cubed? It looks fine for simple search for students. Just for android 
> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwihk7ygxdzOAhUGFpQKHZ_RBpUQFggeMAA&url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dclub.amase.mocubed&usg=AFQjCNF19ew2v3WPP2LVIgqlw_k2SAmwMA
> Pino
> 
> 
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[Jmol-users] (no subject)

[pinostricc...@alice.it]

Dear Friends, has any of you had the chance to use the app on android called 
Mo-Cubed? It looks fine for simple search for students. Just for android 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwihk7ygxdzOAhUGFpQKHZ_RBpUQFggeMAA&url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dclub.amase.mocubed&usg=AFQjCNF19ew2v3WPP2LVIgqlw_k2SAmwMA
Pino


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Re: [Jmol-users] (no subject)

[trematodeo]

So the way to go is to use timeout (or setInterval in javascript). Thanks
Rolf!

On 3 August 2015 at 10:56, Rolf Huehne  wrote:

> On 08/03/2015 03:38 PM, tremato...@gmail.com wrote:
> > I'm doing something like you said:
> >
> > var checkHover;
> > function hoverCallback(a,b,c,d){
> > if(checkHover)
> > clearInterval(checkHover);
> > var res = b.split('.')[0];//get everything until first "."
> > Jmol.script(myJmolOb, 'select '+ res +' ; halo on;');
> >  checkHover = setInterval(function() {
> > Jmol.script(myJmolOb, 'select '+ res +' ; halo off;');
> > }, 1000);
> > }
> >
> >
> > What I did is, every call I cancel the setInterval, then I set the
> > highlight (I'm using halo on here) and finally I start setInterval again.
> > So in the last call (when I move out) the setInterval will not be
> canceled
> > being called after 1 second. It's working.
> >
> > That's really how hovercallback works? This behavior to keep calling the
> > listener also to do not call when move out?
> >
> I obviously didn't remember it correctly and forgot about the timout stuff.
>
> My implementation below works completely within Jmol without any
> Javascript. One advantage of this is that it also works in the Jmol
> application. The 'halo' color is changed to distinguish the 'hover halo'
> from a yellow 'selection halo' which might be already there before the
> 'hover' (setting: "selectionHalos on").
> It took me some time to figure out how to avoid flickering because the
> callback might be fired multiple times for the same atom if the mouse
> pointer rests longer above it. This might not be a problem if
> activating/deactivating the halo is the only action. But in my case
> there was some more stuff which I stripped out here.
> While stripping out the additional stuff I realized that there might
> occur a problem if the 'lastAtomIndexHovered' variable would change too
> fast, although I never observed any problem with it yet. But maybe it
> would be better to provide the atomIndex as a second parameter in the
> "hoverAction('end')" call.
>
> -- Jmolscript hover callback implementation ---
> lastAtomIndexHovered = -1;
> lastHoverUnfinished  = false;
> hoverTimeoutId   = "";
>
> function hoverAction(action) {
>#print "action=" + action + "  hoverId=" + hoverTimeoutId;
>if (hoverTimeoutId != "") {
>  timeout ID @hoverTimeoutId off;
>  hoverTimeoutId = "";
>}
>var switchOff= false;
>var currentSelection = {selected};
>
>if (action == "end") {
>  if (lastHoverUnfinished) {
>switchOff = true;
>  }
>} elseif (action == "start") {
>  if (lastHoverUnfinished) {
>if (lastAtomIndexHovered != _atomhovered) {
>  switchOff = true;
>}
>  }
>}
>
>#print "action=" + action + "  switchOff=" + switchOff + "
> lastHoverUnfinished=" + lastHoverUnfinished + "  lastAtomIndexHovered="
> + lastAtomIndexHovered + "  _atomhovered=" + _atomhovered;
>
>if (switchOff) {
>  if (lastAtomIndexHovered >= 0) {
>select atomindex=@lastAtomIndexHovered;
>color halo yellow;
>halo off;
>  }
>  lastAtomIndexHovered = -1;
>  lastHoverUnfinished  = false;
>}
>
>if (_atomhovered >= 0 && action == "start") {
>  lastAtomIndexHovered = _atomhovered;
>  select atomindex=@lastAtomIndexHovered;
>  color halo cyan;
>  halo on;
>  lastHoverUnfinished  = true;
>  hoverTimeoutId = "hoverEnd_" + now();
>  timeout ID @hoverTimeoutId 1.0 "hoverAction('end')";
>}
>
>select @currentSelection;
> }
>
> set hoverCallback "jmolscript: hoverAction('start');";
> ---
>
> 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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Re: [Jmol-users] (no subject)

[Rolf Huehne]

On 08/03/2015 03:38 PM, tremato...@gmail.com wrote:
> I'm doing something like you said:
>
> var checkHover;
> function hoverCallback(a,b,c,d){
> if(checkHover)
> clearInterval(checkHover);
> var res = b.split('.')[0];//get everything until first "."
> Jmol.script(myJmolOb, 'select '+ res +' ; halo on;');
>  checkHover = setInterval(function() {
> Jmol.script(myJmolOb, 'select '+ res +' ; halo off;');
> }, 1000);
> }
>
>
> What I did is, every call I cancel the setInterval, then I set the
> highlight (I'm using halo on here) and finally I start setInterval again.
> So in the last call (when I move out) the setInterval will not be canceled
> being called after 1 second. It's working.
>
> That's really how hovercallback works? This behavior to keep calling the
> listener also to do not call when move out?
>
I obviously didn't remember it correctly and forgot about the timout stuff.

My implementation below works completely within Jmol without any 
Javascript. One advantage of this is that it also works in the Jmol 
application. The 'halo' color is changed to distinguish the 'hover halo' 
from a yellow 'selection halo' which might be already there before the 
'hover' (setting: "selectionHalos on").
It took me some time to figure out how to avoid flickering because the 
callback might be fired multiple times for the same atom if the mouse 
pointer rests longer above it. This might not be a problem if 
activating/deactivating the halo is the only action. But in my case 
there was some more stuff which I stripped out here.
While stripping out the additional stuff I realized that there might 
occur a problem if the 'lastAtomIndexHovered' variable would change too 
fast, although I never observed any problem with it yet. But maybe it 
would be better to provide the atomIndex as a second parameter in the 
"hoverAction('end')" call.

-- Jmolscript hover callback implementation ---
lastAtomIndexHovered = -1;
lastHoverUnfinished  = false;
hoverTimeoutId   = "";

function hoverAction(action) {
   #print "action=" + action + "  hoverId=" + hoverTimeoutId;
   if (hoverTimeoutId != "") {
 timeout ID @hoverTimeoutId off;
 hoverTimeoutId = "";
   }
   var switchOff= false;
   var currentSelection = {selected};

   if (action == "end") {
 if (lastHoverUnfinished) {
   switchOff = true;
 }
   } elseif (action == "start") {
 if (lastHoverUnfinished) {
   if (lastAtomIndexHovered != _atomhovered) {
 switchOff = true;
   }
 }
   }

   #print "action=" + action + "  switchOff=" + switchOff + " 
lastHoverUnfinished=" + lastHoverUnfinished + "  lastAtomIndexHovered=" 
+ lastAtomIndexHovered + "  _atomhovered=" + _atomhovered;

   if (switchOff) {
 if (lastAtomIndexHovered >= 0) {
   select atomindex=@lastAtomIndexHovered;
   color halo yellow;
   halo off;
 }
 lastAtomIndexHovered = -1;
 lastHoverUnfinished  = false;
   }

   if (_atomhovered >= 0 && action == "start") {
 lastAtomIndexHovered = _atomhovered;
 select atomindex=@lastAtomIndexHovered;
 color halo cyan;
 halo on;
 lastHoverUnfinished  = true;
 hoverTimeoutId = "hoverEnd_" + now();
 timeout ID @hoverTimeoutId 1.0 "hoverAction('end')";
   }

   select @currentSelection;
}

set hoverCallback "jmolscript: hoverAction('start');";
---

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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Re: [Jmol-users] (no subject)

[trematodeo]

I'm doing something like you said:

var checkHover;
function hoverCallback(a,b,c,d){
if(checkHover)
clearInterval(checkHover);
var res = b.split('.')[0];//get everything until first "."
Jmol.script(myJmolOb, 'select '+ res +' ; halo on;');
checkHover = setInterval(function() {
Jmol.script(myJmolOb, 'select '+ res +' ; halo off;');
}, 1000);
}


What I did is, every call I cancel the setInterval, then I set the
highlight (I'm using halo on here) and finally I start setInterval again.
So in the last call (when I move out) the setInterval will not be canceled
being called after 1 second. It's working.

That's really how hovercallback works? This behavior to keep calling the
listener also to do not call when move out?








On 3 August 2015 at 09:27, Ron Mignery  wrote:

> Am 02.08.15 um 20:34 schrieb tremato...@gmail.com:
> >  Hi,
> >
> > I'm trying to create a highlight effect when the user keeps the mouse
> > over a residue, so besides the label I'm also changing the residue color.
> > I'm using hoverCallback to set the color but I also need a hover out to
> > set the color back to the original.
> >
> > 1. Is there a 'hover out' callback or other way to achieve this?
> As far as I remember the 'hover' callback is fired on both events: 'in'
> and 'out'. If you keep track what happened at the last call of your
> callback function you will be able to restore what was done.
> > 2. How can I get the current colors from a residue, for example, get the
> > colors from [SER]679:B.CA  > ?
> >
> Perhaps you could set a timeout in the callback slightly smaller than the
> hover callback repeat interval and clear the highlight when it timed out.
>
>
>
> --
>
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[Jmol-users] (no subject)

[Ron Mignery]

Am 02.08.15 um 20:34 schrieb tremato...@gmail.com:
>  Hi,
>
> I'm trying to create a highlight effect when the user keeps the mouse
> over a residue, so besides the label I'm also changing the residue color.
> I'm using hoverCallback to set the color but I also need a hover out to
> set the color back to the original.
>
> 1. Is there a 'hover out' callback or other way to achieve this?
As far as I remember the 'hover' callback is fired on both events: 'in'
and 'out'. If you keep track what happened at the last call of your
callback function you will be able to restore what was done.
> 2. How can I get the current colors from a residue, for example, get the
> colors from [SER]679:B.CA  > ?
>
Perhaps you could set a timeout in the callback slightly smaller than the
hover callback repeat interval and clear the highlight when it timed out.
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[Jmol-users] (no subject)

[pinostricc...@alice.it]

I updated to jmol-14.3.13_2015.05.08 but nothing seems visible. What can have 
been happened? 
Thanks Pino

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Re: [Jmol-users] (no subject)

[Robert Hanson]

OK.

no 3D canvas in Jmol. But if you use set antialiasDisplay, then the fonts
will be antialised in JSmol. That could be it.

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[Jmol-users] (no subject)

[David Leader]

Bob wrote:

I must be missing something in reading:


*I have now done quite a bit of experimentation with html5/canvas pages of
my own (documentation available on request, but a test page is viewable at
http://motif.gla.ac.uk/JSmolTest/canvasTextCheck.html
;*

*). If things are as straightforward as indicated then the following should
satisfy everyone: *
ctx.font = "12px Helvetica Neue, Arial, sans-serif";
and
ctx.font = "bold 12px Helvetica Neue, Arial, sans-serif";

Windows browsers ignore Helvetica Neue (the current Mac OS default)
and pick up Arial, the Windows default. If there is some way of
testing this on a JSmol canvas I should be interested in trying it or
seeing the result.

Wasn't that a request for Helvetica Neue?


Sorry Bob, we seem to have got our wires crossed. I should have known
better than to try to use gmail for mailing lists. It really is a
nightmare. Only reason for doing so was another list seemed to have
blacklisted my ISP. Anyway...

...things were not that straightforward, and as I discovered after
that initial post. To summarize:

1. Helvetica Neue is the default Mac font on the current OSX Yosemite
(and also on Mavericks) and iOS 8. If you specify sans-serif you get
Helvetica Neue.
2. The default font previously was Lucida Grande, although HN was installed.
3. Apple in iOS 7 went to extreme lengths to support sophisticated
resizable versions of Helvetica Neue, and also allow single-pixel thin
sizes on iOS retina display.
4. Fonts on screen undergo sub-pixel rendering (anti-aliasing) to
smooth them. Apple has always paid more attention to this than
Windows. (When Microsoft started introducing it, many users objected
as they preferred the darker jagged text they were used to, in
preference to the lighter effect of anti-aliasing).
5. Apple has clearly changed its rendering engine between Snow Leopard
and Mavericks in a way that affects the canvas in JSmol, but does not
affect general MacOS X rendering or rendering of text on a canvas.

I have documented some of this at http://motif.gla.ac.uk/JSmolTest/HN/HN.html

I personally am interested in why this is happening - is it something
to do with having a 3d rather than  a 2d canvas for example? - but I'm
not that interested. As far as you are concerned I would forget it -
there are more important technical problems that deserve your
attention than this.

You say:

===

Something is too subtle there for me -- they all look fine. Except in the
cases
where you see text running over the text box, that's a bug in Safari
misreporting
===

It may be too subtle for you, but it is there. I have an eye for these
things and can see the difference between Helvetica Neue and Avenir
immediately. I have blown them up, measured them, analysed the colours
and could explain it to you, but you'd be as well to take my word for
it. It's not a big difference, but I'll serve it on my site and it
will give any Mac user a slightly better experience, whether or not
they could analyse it. It's all about subconscious perception.

The bottom line is that Java Applets are clearly doomed and unlikely
to see 2016 (I'm sad about that as some of my own die with them), but
Jmol lives on as JSmol and my own Motivated Proteins site lives on
with it. Thank you again for that.

JSmol may be slower than Jmol (and Firefox/Mac does not seem too happy
with it sometimes) but JavaScript and computers will get faster, and
browsers will be continue to improve their optimization for
JavaScript, so time will cure the current problems.

David

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Re: [Jmol-users] (no subject)

[Robert Hanson]

I'm sorry. I broke JSmol.min.nojq.js on Aug. 30 when I modified the way the
date/version business is passed to JSmol.

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.30.zip

Or remove the first-line references to Jmol.___ (three commands)
inJSmol.min.nojq.js

Bob

​
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Re: [Jmol-users] (no subject)

[Otis Rothenberger]

Pino,

I'm not sure I understand all of your .js files, but this one appears to 
be missing:


src="http://pinostriccoli.altervista.org/wp-content/Jmol2.js";

Otis

pino.stricc...@libero.it 
September 30, 2014 at 6:56 PM
Bob, i updated the Jsmol to the version 14.3.7 and the installation 
works like
here http://pinostriccoli.altervista.org/html5/simple2.htm. It 
disappear all
when i run from my site. U can check any page 
http://pinostriccoli.altervista.

org/?p=4681
As if no files loaded in head section that is this
src="http://pinostriccoli.altervista.org/wp-
content/JSmol.min.nojq.js">
src="http://pinostriccoli.altervista.org/wp-
content/Jmol2.js">

var Info = {
width: 350,
height: 350,
serverURL: "http://pinostriccoli.altervista.org/html5/php/jsmol.php";,
use: "HTML5",
j2sPath: "html5/j2s",
console: "none",
script: "load wp-content/alpha.pdb; background black"
}

I did not touche code in my pages. Did i miss some important file?
Pino


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--
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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Bob, i updated the Jsmol to the version 14.3.7 and the installation works like 
here http://pinostriccoli.altervista.org/html5/simple2.htm. It disappear all 
when i run from my site. U can check any page http://pinostriccoli.altervista.
org/?p=4681
As if no files loaded in head section that is this
http://pinostriccoli.altervista.org/wp-
content/JSmol.min.nojq.js">
http://pinostriccoli.altervista.org/wp-
content/Jmol2.js">

var Info = {
width: 350,
height: 350,
serverURL: "http://pinostriccoli.altervista.org/html5/php/jsmol.php";,
use: "HTML5",
j2sPath: "html5/j2s",
console: "none",
script: "load wp-content/alpha.pdb; background black"
}

I did not touche code in my pages. Did i miss some important file?
Pino


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Re: [Jmol-users] (no subject)

[Robert Hanson]

There were some problems with JSME -- try JSmol 14.3.7 and see how it works
-- http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.26.zip

On Fri, Sep 26, 2014 at 10:44 AM, pino.stricc...@libero.it <
pino.stricc...@libero.it> wrote:

>
> Hi .. I am trying to fix jsme with jsmol in the folloqing page
> http://pinostriccoli.altervista.org/?page_id=7078
> When i switch to 2d, JSME, it fails to load the applet.
> The jsme works by itself at http://pinostriccoli.altervista.
> org/html5/jsme/JSME.html
> Any guess?
> Pino
>
>
>
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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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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Hi .. I am trying to fix jsme with jsmol in the folloqing page
http://pinostriccoli.altervista.org/?page_id=7078
When i switch to 2d, JSME, it fails to load the applet. 
The jsme works by itself at http://pinostriccoli.altervista.
org/html5/jsme/JSME.html
Any guess? 
Pino


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Re: [Jmol-users] (no subject)

[Robert Hanson]

same here for http://pinostriccoli.altervista.org/html5/jsmol.htm?_USE=HTML5

On Thu, Sep 18, 2014 at 2:08 PM, Angel Herráez  wrote:

> Pino, that URL loads without problem in my Firefox
>
> Try clearing your cache
>
> On 18 Sep 2014 at 20:14, pino.stricc...@libero.it wrote:
> > i am aalways having  a bloank page http://pinostriccoli.altervista.
> > org/html5/jsmol.htm?_USE=HTML5
>
>
>
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Re: [Jmol-users] (no subject)

[Angel Herráez]

Pino, that URL loads without problem in my Firefox

Try clearing your cache

On 18 Sep 2014 at 20:14, pino.stricc...@libero.it wrote:
> i am aalways having  a bloank page http://pinostriccoli.altervista.
> org/html5/jsmol.htm?_USE=HTML5 


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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Bob, i am having some problems on loading jsmol. I downloaded the version 
present on sourceforge.
i am aalways having  a bloank page http://pinostriccoli.altervista.
org/html5/jsmol.htm?_USE=HTML5 
I was trying to apgrade the jsmol version. 
This will be wher my blog will point
Pino

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Re: [Jmol-users] (no subject)

[Angel Herráez]

Ron, the question is: who would run the Javascript? There is no JS 
interpreter if you are not in a webpage


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Re: [Jmol-users] (no subject)

[Robert Hanson]

I don't see the Jmol application as much more than a development tool. The
target environment for Jmol is a web page.


On Fri, Jan 24, 2014 at 11:18 PM, Ron Mignery  wrote:

> I use the application, not the applet. Can I use the javascipt command
> there? The documentation describes the javascript command as applet only.
>
> On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson  wrote
>
> >I would just use the javascript command to introduce your own audio
> >components.
>
>
> >On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery  wrote:
>
> >> Could a play  command similar to the Java play function be
> >> added to scripting?  This would allow clicks and beeps or even entire
> >> narrations to be added to Jmol animations.  Hopefully it would run in a
> >> separate thread.
>
>
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[Jmol-users] (no subject)

[Ron Mignery]

I use the application, not the applet. Can I use the javascipt command
there? The documentation describes the javascript command as applet only.

On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson  wrote

>I would just use the javascript command to introduce your own audio
>components.


>On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery  wrote:

>> Could a play  command similar to the Java play function be
>> added to scripting?  This would allow clicks and beeps or even entire
>> narrations to be added to Jmol animations.  Hopefully it would run in a
>> separate thread.
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[Jmol-users] (no subject)

[carlon]

car...@cerm.unifi.it


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Re: [Jmol-users] (no subject)

[Jaime Prilusky]

Chrome 31.0.1650.57 and Safari Version 7.0 (9537.71) on Mac 10.9 also gave 
format error, most probably the same you got.

Simply Javascript on Firefox (Gecko engine) runs under different rules than on 
Chrome/Safari (WebKit engine). 

Jaim

On Nov 26, 2013, at 7:14 PM, pino.stricc...@libero.it wrote:

> Can anybody explain to me this error i find on this page http://pinostriccoli.
> altervista.org/?p=5589?
> On firefox (windows or linux) it works ok. In Chrome (windows or Linux) gives 
> me unrecognised format error. 
> What happens? any idea? 
> Pino
> 
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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Can anybody explain to me this error i find on this page http://pinostriccoli.
altervista.org/?p=5589?
On firefox (windows or linux) it works ok. In Chrome (windows or Linux) gives 
me unrecognised format error. 
What happens? any idea? 
Pino

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Re: [Jmol-users] (no subject)

[Angel Herráez]

No, we don't have it in the Wiki.
I remember some former thread about MathJax but did not take note.

I will try to do it some day
I think there is a page on compatibility with other 
frameworks/libraries, it could go there




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Re: [Jmol-users] (no subject)

[Robert Hanson]

Do we have that on the wiki yet, Angel? If not, we need to add it. Since
MathJax actually rewrites the entire page after loading, you have to make
sure your Jmol applet is added within a script that runs only after MathJax
is complete. Not sure if MathJax has a callback on that, but there is a div
on the page that is hidden and is reporting MathJax progress.

Here is a rendition of that prior message on this list, updated a bit for
newer JSmol.min.js versions.

It's a pretty simple solution. Really what the problem is is that both Jmol
and MathJax are competing for the AJAX processing. For compatibility with
MathJax, make sure:

1) you are using dynamic loading of the applet
-- no 

[Jmol-users] (no subject)

[Carl McBride]

This is not really a bug, I am just looking for an idiots guide to running 
both JSmol (jmol-13.2.8) in conjunction with MathJax (release branch v2.2) 
on a MediaWiki (1.21.2) site without getting a red [Math Processing 
Error].


All the best,
carl





Dr. Carl McBride

Departamento de Ciencias y Técnicas Fisicoquímicas
Facultad de Ciencias
Universidad Nacional de Educación a Distancia (UNED)
28040 Madrid
Spain

friedel.uned.es/carlmcbride.html

www.SklogWiki.org


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Re: [Jmol-users] (no subject)

[Angel Herráez]

Ciao Pino

http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Functions_that_s
et_CSS_rules
explains it.

> I found jmol.setAppletCss. Where should I insert the script and what can be 
> the exat sintax?

Not exact, but something like this:

Before the call to getJmolApplet:
   Jmol.setAppletCss(".toLeft")
as long as you have defined the css code for class "toLeft"
or
   Jmol.setAppletCss("style='float:left'")



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Re: [Jmol-users] (no subject)

[Robert Hanson]

The jQuery way to do that would be somethng like this:


$("#jmolApplet0_appletinfotablediv").css({top:"5px",left:"400px"})

where "jmolApplet0" is the name of my applet.

Bob



On Mon, Sep 16, 2013 at 4:12 PM, pino.stricc...@libero.it <
pino.stricc...@libero.it> wrote:

> Hi Friends, i am trying to format the page
> http://pinostriccoli.altervista.org/?
> p=6434
> and i want the molecule floating to the left so that written text gos to
> its
> right.
> I found jmol.setAppletCss. Where should I insert the script and what can be
> the exat sintax?
> thanks
> Pino
>
>
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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Hi Friends, i am trying to format the page http://pinostriccoli.altervista.org/?
p=6434
and i want the molecule floating to the left so that written text gos to its 
right. 
I found jmol.setAppletCss. Where should I insert the script and what can be 
the exat sintax?
thanks  
Pino

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Re: [Jmol-users] (no subject)

[Angel Herráez]

Hello Pino

I looked at your source code.
Some things have changed, particularly integration with jQuery (and that 
deals with the AJAX methods for loading files from remote servers, as fas as 
I understand).
Instead of calling several JS files, you should just call jsmol.min.js
See the Wiki > JSmol page for more details



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Re: [Jmol-users] (no subject)

[Rolf Huehne]

On 08/27/2013 06:56 PM, pino.stricc...@libero.it wrote:
> After a long break from JSmol, i decided to upload the last version of JSmol 
> and continue working on my pages, but i found some problems with these pages 
> http://pinostriccoli.altervista.org/html5/index.htmlwhen trying to load 
> molecoles in pdb. It seems loading just mol and xyz files.I have the error 
> file reader not found  Any suggestion?did i do some mistake in uploading?
> Thanks a lotPino
>
Your update didn't work correctly. The JSmol version that is shown in 
the JSmol menu on your page is '13.1.12_dev' but the latest is at least 
13.3.4. You should try updating again.

Regards,
Rolf
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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

After a long break from JSmol, i decided to upload the last version of JSmol 
and continue working on my pages, but i found some problems with these pages 
http://pinostriccoli.altervista.org/html5/index.htmlwhen trying to load 
molecoles in pdb. It seems loading just mol and xyz files.I have the error file 
reader not found  Any suggestion?did i do some mistake in uploading? 
Thanks a lotPino

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Re: [Jmol-users] (no subject)

[Angel Herráez]

Hi Pino

Yes, this problem has been there always with reading MOLfile data. As 
Bob says, using the JME format for the transfer fixes it. You can see 
both demonstrated in my page (compare the 2 buttons)
http://biomodel.uah.es/en/DIY/JME/JME.htm

If you still need to use MOL (as I do in my pages that do not use JME 
but other editors), the problem only affects a few very symmetrical 
molecules like cyclohexane and tert-butane.

I just had the idea of changing the Z coord of one of the atoms (to 
break the symmetry) and it works for cyclohexane, see
http://biomodel.uah.es/en/DIY/JME/JME2.htm

but not for tert-butane as Jmol wrongly interprets tertiary carbons 
as planar (there was discussion about this some time ago and I guess 
some conclusion that I cannot remember, but I could not find a 
solution to apply to my page --but this is another issue.)


PS: Could you please ammend my name in your page? Thanks



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Re: [Jmol-users] (no subject)

[Robert Hanson]

This worked:


jmolLoadInlineScript( gid('editor').jmeFile(),"")


On Fri, Sep 21, 2012 at 8:40 AM, Robert Hanson  wrote:

> It works at
> http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htmwithout a 
> problem. I'll take a look at your page to see what is going on
> there.
>
> On Fri, Sep 21, 2012 at 7:25 AM, pino.stricc...@libero.it <
> pino.stricc...@libero.it> wrote:
>
>> Hi everybody. I have a simple issue. A mistake in rendering cicloexane
>> ring from JME to Jmol.
>>
>> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure
>> the error. I remember being an old issue with Jmol. It appears in Jmol13,
>> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr
>> ring for cycloexane. What happens ?
>>
>> Pino
>>
>>
>>
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>>
>>
>
>
> --
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> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
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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-users] (no subject)

[Robert Hanson]

try using the JME output rather than the MOL file output.

On Fri, Sep 21, 2012 at 8:40 AM, Robert Hanson  wrote:

> It works at
> http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htmwithout a 
> problem. I'll take a look at your page to see what is going on
> there.
>
> On Fri, Sep 21, 2012 at 7:25 AM, pino.stricc...@libero.it <
> pino.stricc...@libero.it> wrote:
>
>> Hi everybody. I have a simple issue. A mistake in rendering cicloexane
>> ring from JME to Jmol.
>>
>> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure
>> the error. I remember being an old issue with Jmol. It appears in Jmol13,
>> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr
>> ring for cycloexane. What happens ?
>>
>> Pino
>>
>>
>>
>> --
>> Got visibility?
>> Most devs has no idea what their production app looks like.
>> Find out how fast your code is with AppDynamics Lite.
>> http://ad.doubleclick.net/clk;262219671;13503038;y?
>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>> ___
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>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Got visibility?
Most devs has no idea what their production app looks like.
Find out how fast your code is with AppDynamics Lite.
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Re: [Jmol-users] (no subject)

[Robert Hanson]

Oh, one  thing I see is that you are using an older JME applet. Try the one
in http://chemapps.stolaf.edu/jmol/docs/examples-12  Although I don't think
that is the problem.

On Fri, Sep 21, 2012 at 7:25 AM, pino.stricc...@libero.it <
pino.stricc...@libero.it> wrote:

> Hi everybody. I have a simple issue. A mistake in rendering cicloexane
> ring from JME to Jmol.
>
> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure
> the error. I remember being an old issue with Jmol. It appears in Jmol13,
> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr
> ring for cycloexane. What happens ?
>
> Pino
>
>
>
> --
> Got visibility?
> Most devs has no idea what their production app looks like.
> Find out how fast your code is with AppDynamics Lite.
> http://ad.doubleclick.net/clk;262219671;13503038;y?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Got visibility?
Most devs has no idea what their production app looks like.
Find out how fast your code is with AppDynamics Lite.
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Re: [Jmol-users] (no subject)

[Robert Hanson]

It works at
http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htm without
a problem. I'll take a look at your page to see what is going on there.

On Fri, Sep 21, 2012 at 7:25 AM, pino.stricc...@libero.it <
pino.stricc...@libero.it> wrote:

> Hi everybody. I have a simple issue. A mistake in rendering cicloexane
> ring from JME to Jmol.
>
> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure
> the error. I remember being an old issue with Jmol. It appears in Jmol13,
> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr
> ring for cycloexane. What happens ?
>
> Pino
>
>
>
> --
> Got visibility?
> Most devs has no idea what their production app looks like.
> Find out how fast your code is with AppDynamics Lite.
> http://ad.doubleclick.net/clk;262219671;13503038;y?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Got visibility?
Most devs has no idea what their production app looks like.
Find out how fast your code is with AppDynamics Lite.
http://ad.doubleclick.net/clk;262219671;13503038;y?
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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Hi everybody. I have a simple issue. A mistake in rendering cicloexane ring 
from JME to Jmol. At my page http://pinostriccoli.altervista.org/?page_id=873, 
it is sure the error. I remember being an old issue with Jmol. It appears in 
Jmol13, and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. 
Palanr ring for cycloexane. What happens ?Pino
 --
Got visibility?
Most devs has no idea what their production app looks like.
Find out how fast your code is with AppDynamics Lite.
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Re: [Jmol-users] (no subject)

[Robert Hanson]

I don't see the crashing. What's the error report?

x = getProperty("atomInfo")

gets that into a model.

$ load $caffeine
print getProperty("atomInfo")[3]
$

_ipt:2
atomIndex:2
atomno:3
bondCount:3
clickabilityFlags:12
colix:-32762
color:[x909090]
coord:{1.7906001 0.2081 0.0010}
element:carbon
elemno:6
formalCharge:0
info:C3 #3
model:1
partialCharge:0.0
radius:0.8084
shape:trigonal planar
spacefill:0.391
sym:C
visibilityFlags:13
visible:true
x:1.7906001
y:0.2081
z:0.0010


$ print getProperty("atomInfo")[3]["atomno"]

3

It's more efficient, if you only want one value, to put it all in the
quotes:

$ print getProperty("atomInfo[3][color]")
[x909090]

and if you skip the [3], you get a list over all the atoms (in this case)

$ print getProperty("atomInfo[color]")
[x3050f8]
[x909090]
[x909090]
[xff0d0d]
...

Bob


On Thu, Jul 26, 2012 at 7:05 AM, Martin Hediger  wrote:

> Dear Jmol Users
> If I load a PDB structure into the Jmol application (not the Jmol
> applet) and use
>
> getProperty "atomInfo", "1.1"
>
> I receive the output
>
> atomInfo*List[0]
>
> in bold blue font. However, when I just use
>
> getProperty "atomInfo"
>
> the application crashes.
>
> I have two questions:
> 1) In the Jmol application, how can I assign the *List[0] content to a
> variable and access its elements? Whats the Jmol syntax for this?
> 2) What do the '*' and the [0] mean in this context?
>
> Thanks for help.
> Martin
>
>
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>



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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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[Jmol-users] (no subject)

[Martin Hediger]

Dear Jmol Users
If I load a PDB structure into the Jmol application (not the Jmol 
applet) and use

getProperty "atomInfo", "1.1"

I receive the output

atomInfo*List[0]

in bold blue font. However, when I just use

getProperty "atomInfo"

the application crashes.

I have two questions:
1) In the Jmol application, how can I assign the *List[0] content to a 
variable and access its elements? Whats the Jmol syntax for this?
2) What do the '*' and the [0] mean in this context?

Thanks for help.
Martin

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[Jmol-users] (no subject)

[pieremanuele canepa]

Dear All,

Can you  show me the Jmol command  to add a new atom knowing its fractional
or Cartesian coordinates?

Thanks a lot, Piero

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Re: [Jmol-users] (no subject)

[Mio_libero]

  One more think, Angel. I tried JME, Jpaintdraw with PCl5 molecule. The 
Jmol optimization is not trigonal bipyramidal as expected. Am i wrong or 
is it an issue in JMOL?
Pino

>>I already have JME working in my page on my weblog, Actually i can see
>> the molecule in 3d on molinspiration.com. I would like to use just Jmol
>> in the same page with JME or Jchempaint.
>> What do I need to display the two applets working and connected on the
>> same page ?
> Jmol will accept either the JME string or a MOL exported from JME. You can 
> extract the JME
> into a javascript variable, then use that to fill Jmol applet using 
> JmolLoadInline()
> Check the source of my page   http://biomodel.uah.es/en/DIY/JME/JME.htm
> or Bob's page that does the same
> http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm
>
> I'm not sure however about how all this can be fit into the blog. Have you 
> read the Jmol Wiki
> section about implementing Jmol in blogs?
>
>
> --
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
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Re: [Jmol-users] (no subject)

[Mio_libero]

  Thanks Angel, i will read wiki about this and adapt the code to my 
case. I think it will be a bit difficult with blog but i already did 
something in my blog, so i hope i can succed. Pino

Il 08/10/2010 0.15, Angel Herráez ha scritto:
>>I already have JME working in my page on my weblog, Actually i can see
>> the molecule in 3d on molinspiration.com. I would like to use just Jmol
>> in the same page with JME or Jchempaint.
>> What do I need to display the two applets working and connected on the
>> same page ?
> Jmol will accept either the JME string or a MOL exported from JME. You can 
> extract the JME
> into a javascript variable, then use that to fill Jmol applet using 
> JmolLoadInline()
> Check the source of my page   http://biomodel.uah.es/en/DIY/JME/JME.htm
> or Bob's page that does the same
> http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm
>
> I'm not sure however about how all this can be fit into the blog. Have you 
> read the Jmol Wiki
> section about implementing Jmol in blogs?
>
>
> --
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
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Re: [Jmol-users] (no subject)

[Angel Herráez]

>   I already have JME working in my page on my weblog, Actually i can see 
> the molecule in 3d on molinspiration.com. I would like to use just Jmol 
> in the same page with JME or Jchempaint.
> What do I need to display the two applets working and connected on the 
> same page ?

Jmol will accept either the JME string or a MOL exported from JME. You can 
extract the JME 
into a javascript variable, then use that to fill Jmol applet using 
JmolLoadInline()
Check the source of my page http://biomodel.uah.es/en/DIY/JME/JME.htm
or Bob's page that does the same
http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm

I'm not sure however about how all this can be fit into the blog. Have you read 
the Jmol Wiki 
section about implementing Jmol in blogs?


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Re: [Jmol-users] (no subject)

[Angel Herráez]

> i am trying to implement in my blog (http://pinostriccoli.altervista.org) JME 
> TO JMOL (or 
> JChempaint as in http://biomodel.uah.es/en/DIY/JChemPaint3/draw.en.htm), so 
> that the two 
> applets will be displayed in just one window. 
> At the moment there is a link to Molinspiration that i would like to 
> change.Where can i download 
> the files ? 

Which files, Pino?   JME?

http://www.molinspiration.com/jme/index.html
points you to "How to get JME"
http://www.molinspiration.com/jme/getjme.html
which says
"The latest version of JME editor applet may be obtained for non-commercial use 
directly 
from its author Peter Ertl [...] To request JME send an email ..."







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[Jmol-users] (no subject)

[pino.stricc...@libero.it]

Hi, i am trying to implement in my blog (http://pinostriccoli.altervista.org) 
JME TO JMOL (or JChempaint as in 
http://biomodel.uah.es/en/DIY/JChemPaint3/draw.en.htm), so that the two applets 
will be displayed in just one window. At the moment there is a link to 
Molinspiration that i would like to change.Where can i download the files ? 
ThanksPino
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[Jmol-users] (no subject)

[P . Canepa]

Thanks Jonathan

 I got your script and I was trying to use it.

My HTML page has  the script set like that 



var Colorscript = new Array (setAtomColor);
jmolColorPickerBox(Colorscript, 'rgb(100,100,100)')";


The array Colorscript should be the array  which include the name of the 
function to call, see below

the function setAtomColor() is  written as :

 var atomColor = "";
  function elementSelected(element){
   setValue("select none; halo off; label off");
   setValue("select "  + element + "; halo on; label on");

   atomColor = "' color " + element;   
   return atomColor;
  }



 function setAtomColor (rgbCodeStr, Colorscript , jmolApplet0, atomColor){
   var finalColor =  " " + atomColor + " " + rgbCodeStr + " ";
   return finalColor;
 }
 
I think I got your explanation wrong  in the headings of your script. Is the 
rgbCodeStr the color selected by  jmolColorPickerBox ?
Thanks a lot, Piero





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Please consider the environment before printing this e-mail.

Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
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Re: [Jmol-users] (no subject)

[Robert Hanson]

show me the page.

On Thu, Apr 15, 2010 at 10:45 AM, P.Canepa  wrote:

>Quick mind Bob
> my functions are. Then what's wrong ?
>
> Thanks, Piero
>
> function loadModels(selectbox){
>
>   removeAllModels()
> var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")
>
>  if(!Info){
>  alert("No models available")
>   return
>   }
>
>  for(var i=0; i< Info.length; i++)
>   addOption(document.modelsVib.models, i + " " + Info[i].name, i + 2);
> }
>
> function myMessageCallback(a,m) {
> m = "" + m
> // important to do this to change from Java string to JavaScript string
> if (m.indexOf("DONE") == 0) loadModels()
> }
>
>function onClickLoadStruc() {
> jmolScriptWait("load ?;  background white; set 
> messageCallback'myMessageCallback';messageDONE");
> }
>
> --
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
> e-mail: pc...@kent.ac.uk
> mobile: +44 (0) 7772-9756456
> ---------------
>
>  --
> *From:* P.Canepa [pc...@kent.ac.uk]
> *Sent:* Thursday, April 15, 2010 4:42 PM
>
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] (no subject)
>
> Are you sure because nothing seems to change!
>
> --
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
> e-mail: pc...@kent.ac.uk
> mobile: +44 (0) 7772-9756456
> ---
>
>  --
> *From:* Robert Hanson [hans...@stolaf.edu]
> *Sent:* Thursday, April 15, 2010 4:30 PM
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] (no subject)
>
>  Ah, ok. I remember. You are getting an access violation because the
> thread that runs the load command cannot also run the JavaScript command.
>
> Problem: I want to load a file using the dialog in the signed applet and
> then after that run some JavaScript.
>
> Solution: You must use the message callback mechanism to let your page know
> that the loading is done, and from THAT function, run your JavaScript:
>
>
> function loadModels(){
>  removeAllModels()
>   var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")
> .. etc...
> }
>
> function myMessageCallback(a,m) {
>  m = "" + m
> // important to do this to change from Java string to JavaScript string
>  if (m.indexOf("DONE") == 0) loadModels()
> }
>
> function onClickLoadStruc() {
>   jmolScript("load ?;  background white;set messageCallback
> 'myMessageCallback';message DONE")
> }
>
>
>
>
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
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Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[P . Canepa]

Quick mind Bob
my functions are. Then what's wrong ?

Thanks, Piero

function loadModels(selectbox){
  removeAllModels()
var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")

 if(!Info){
 alert("No models available")
  return
  }

 for(var i=0; i< Info.length; i++)
  addOption(document.modelsVib.models, i + " " + Info[i].name, i + 2);
}

function myMessageCallback(a,m) {
m = "" + m
// important to do this to change from Java string to JavaScript string
if (m.indexOf("DONE") == 0) loadModels()
}

   function onClickLoadStruc() {
jmolScriptWait("load ?;  background white; set messageCallback 
'myMessageCallback';message DONE");
}

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: P.Canepa [pc...@kent.ac.uk]
Sent: Thursday, April 15, 2010 4:42 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

Are you sure because nothing seems to change!

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, April 15, 2010 4:30 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

Ah, ok. I remember. You are getting an access violation because the thread that 
runs the load command cannot also run the JavaScript command.

Problem: I want to load a file using the dialog in the signed applet and then 
after that run some JavaScript.

Solution: You must use the message callback mechanism to let your page know 
that the loading is done, and from THAT function, run your JavaScript:


function loadModels(){
 removeAllModels()
  var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")
.. etc...
}

function myMessageCallback(a,m) {
 m = "" + m
// important to do this to change from Java string to JavaScript string
 if (m.indexOf("DONE") == 0) loadModels()
}

function onClickLoadStruc() {
  jmolScript("load ?;  background white;set messageCallback 
'myMessageCallback';message DONE")
}




Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[P . Canepa]

Are you sure because nothing seems to change!

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, April 15, 2010 4:30 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

Ah, ok. I remember. You are getting an access violation because the thread that 
runs the load command cannot also run the JavaScript command.

Problem: I want to load a file using the dialog in the signed applet and then 
after that run some JavaScript.

Solution: You must use the message callback mechanism to let your page know 
that the loading is done, and from THAT function, run your JavaScript:


function loadModels(){
 removeAllModels()
  var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")
.. etc...
}

function myMessageCallback(a,m) {
 m = "" + m
// important to do this to change from Java string to JavaScript string
 if (m.indexOf("DONE") == 0) loadModels()
}

function onClickLoadStruc() {
  jmolScript("load ?;  background white;set messageCallback 
'myMessageCallback';message DONE")
}




Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[Robert Hanson]

Ah, ok. I remember. You are getting an access violation because the thread
that runs the load command cannot also run the JavaScript command.

Problem: I want to load a file using the dialog in the signed applet and
then after that run some JavaScript.

Solution: You must use the message callback mechanism to let your page know
that the loading is done, and from THAT function, run your JavaScript:


function loadModels(){
 removeAllModels()
  var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")
.. etc...
}

function myMessageCallback(a,m) {
 m = "" + m
// important to do this to change from Java string to JavaScript string
 if (m.indexOf("DONE") == 0) loadModels()
}

function onClickLoadStruc() {
  jmolScript("load ?;  background white;set messageCallback
'myMessageCallback';message DONE")
}




Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[P . Canepa]

I realized that the file is correctly read with  jmolScript("load ?  ")  
wherever it is, whereas it has to be in the same directory as the applet if the 
command jmolScriptWait("load ?  ") . Why ?
How can I solve it ?
What I am tiring to do is an online visualizer. So I cannot set a set 
<http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#set_defaultdirectory> 
defaultDirectory as the user browses the file he likes.

Thanks

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: P.Canepa [pc...@kent.ac.uk]
Sent: Thursday, April 15, 2010 3:56 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

It's strange because all work if I use the normal  jmolScript as below
function onClickLoadStruc() {
  jmolScript("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

This just happens when I employ  jmolScriptWait()


--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Paul Pillot [paul.pil...@ac-orleans-tours.fr]
Sent: Thursday, April 15, 2010 3:54 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

make sure the applet and the files are located in the same directory.
Paul
Le 15 avr. 2010 à 16:34, P.Canepa a écrit :

Te error I see on the jmol deck is java.Security.AccessControlException: 
access.denied (java.io.FilePermission ...
this happens per each file? How comes ?

all the best, Piero

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

Re: [Jmol-users] (no subject)

[P . Canepa]

It's strange because all work if I use the normal  jmolScript as below
function onClickLoadStruc() {
  jmolScript("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

This just happens when I employ  jmolScriptWait()


--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Paul Pillot [paul.pil...@ac-orleans-tours.fr]
Sent: Thursday, April 15, 2010 3:54 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

make sure the applet and the files are located in the same directory.
Paul
Le 15 avr. 2010 à 16:34, P.Canepa a écrit :

Te error I see on the jmol deck is java.Security.AccessControlException: 
access.denied (java.io.FilePermission ...
this happens per each file? How comes ?

all the best, Piero

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

Re: [Jmol-users] (no subject)

[Paul Pillot]

make sure the applet and the files are located in the same directory.
Paul
Le 15 avr. 2010 à 16:34, P.Canepa a écrit :

> Te error I see on the jmol deck is java.Security.AccessControlException: 
> access.denied (java.io.FilePermission ...
> this happens per each file? How comes ?
>  
> all the best, Piero
>  
> -- 
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] (no subject)

[P . Canepa]

Te error I see on the jmol deck is java.Security.AccessControlException: 
access.denied (java.io.FilePermission ...
this happens per each file? How comes ?

all the best, Piero

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: P.Canepa [pc...@kent.ac.uk]
Sent: Thursday, April 15, 2010 3:19 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

Dear Bob,

I tried this one because it looks to me the more feasible. This gives me that 
error I told you.

Thanks Piero

function onClickLoadStruc() {
  jmolScriptWait("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, April 15, 2010 1:44 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

what last one doesn't, and what comes up with what sort of error?

On Thu, Apr 15, 2010 at 7:02 AM, P.Canepa 
mailto:pc...@kent.ac.uk>> wrote:
The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why 
?

Thanks

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu<mailto:hans...@stolaf.edu>]
Sent: Thursday, April 15, 2010 12:30 PM

To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Subject: Re: [Jmol-users] (no subject)

   OnClick='jmolScript("load ?; script scripts/name.spt;  background 
white") + removeAllModels() + loadModels()'

adds function returns in JavaScript. I think you want semicolons. Generally 
good programming is to only have a single function in the onclick:

   OnClick='onClickLoadStruc()'


and then

function onClickLoadStruc() {
  jmolScript("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Remember that jmolScript() is asynchronous -- it queues the load command but 
continues immediately. You want:

function onClickLoadStruc() {
  jmolScriptWait("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Bob


Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[P . Canepa]

Dear Bob,

I tried this one because it looks to me the more feasible. This gives me that 
error I told you.

Thanks Piero

function onClickLoadStruc() {
  jmolScriptWait("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, April 15, 2010 1:44 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

what last one doesn't, and what comes up with what sort of error?

On Thu, Apr 15, 2010 at 7:02 AM, P.Canepa 
mailto:pc...@kent.ac.uk>> wrote:
The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why 
?

Thanks

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu<mailto:hans...@stolaf.edu>]
Sent: Thursday, April 15, 2010 12:30 PM

To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Subject: Re: [Jmol-users] (no subject)

   OnClick='jmolScript("load ?; script scripts/name.spt;  background 
white") + removeAllModels() + loadModels()'

adds function returns in JavaScript. I think you want semicolons. Generally 
good programming is to only have a single function in the onclick:

   OnClick='onClickLoadStruc()'


and then

function onClickLoadStruc() {
  jmolScript("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Remember that jmolScript() is asynchronous -- it queues the load command but 
continues immediately. You want:

function onClickLoadStruc() {
  jmolScriptWait("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Bob


Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[Robert Hanson]

what last one doesn't, and what comes up with what sort of error?

On Thu, Apr 15, 2010 at 7:02 AM, P.Canepa  wrote:

>The last one doesn't work. It comes up with an error JmolApplet0,,,
> Zapped! why ?
>
> Thanks
>
> --
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
> e-mail: pc...@kent.ac.uk
> mobile: +44 (0) 7772-9756456
> ---
>
>  --
> *From:* Robert Hanson [hans...@stolaf.edu]
> *Sent:* Thursday, April 15, 2010 12:30 PM
>
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] (no subject)
>
> OnClick='jmolScript("load ?; script scripts/name.spt;  background
> white") + removeAllModels() + loadModels()'
>
> adds function returns in JavaScript. I think you want semicolons. Generally
> good programming is to only have a single function in the onclick:
>
>OnClick='onClickLoadStruc()'
>
>
> and then
>
> function onClickLoadStruc() {
>   jmolScript("load ?; script scripts/name.spt;  background white")
>   removeAllModels()
>   loadModels()
> }
>
> Remember that jmolScript() is asynchronous -- it queues the load command
> but continues immediately. You want:
>
> function onClickLoadStruc() {
>   jmolScriptWait("load ?; script scripts/name.spt;  background white")
>   removeAllModels()
>   loadModels()
> }
>
> Bob
>
>
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[P . Canepa]

The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why 
?

Thanks

--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---


From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, April 15, 2010 12:30 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] (no subject)

   OnClick='jmolScript("load ?; script scripts/name.spt;  background 
white") + removeAllModels() + loadModels()'

adds function returns in JavaScript. I think you want semicolons. Generally 
good programming is to only have a single function in the onclick:

   OnClick='onClickLoadStruc()'


and then

function onClickLoadStruc() {
  jmolScript("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Remember that jmolScript() is asynchronous -- it queues the load command but 
continues immediately. You want:

function onClickLoadStruc() {
  jmolScriptWait("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Bob


Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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

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

Re: [Jmol-users] (no subject)

[Robert Hanson]

OnClick='jmolScript("load ?; script scripts/name.spt;  background
white") + removeAllModels() + loadModels()'

adds function returns in JavaScript. I think you want semicolons. Generally
good programming is to only have a single function in the onclick:

   OnClick='onClickLoadStruc()'


and then

function onClickLoadStruc() {
  jmolScript("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Remember that jmolScript() is asynchronous -- it queues the load command but
continues immediately. You want:

function onClickLoadStruc() {
  jmolScriptWait("load ?; script scripts/name.spt;  background white")
  removeAllModels()
  loadModels()
}

Bob


Robert M. Hanson
Professor of Chemistry
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1520 St. Olaf Ave.
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[Jmol-users] (no subject)

[P . Canepa]

Dear all,

In the page I am working on  I create a button to load new files as below:



function loadModels() is expected to load on an external list all the models  
called within the first JmolScript(load ?  ).  loadModels() just reads 
models from the previous structure and not from the  latest.
Do you know how to solve his problem? Does exist a way to let the javascript be 
executed sequentially as they are written? for instance  jmolScript("load ?; 
script scripts/name.spt;  background white") + removeAllModels() + loadModels() 
. Stick to the sequence 

Thanks a lot, Piero
Function loadModels() is

function loadModels(selectbox){
var Info = jmolGetPropertyAsArray("auxiliaryInfo.models")
 if(!Info){
 alert("No models available")
  return
  }
 for(var i=0; i< Info.length; i++)
  addOption(document.modelsVib.models, i + " " + Info[i].name, i + 2);
  }

function addOption(selectbox,text,value)
  {
  var optn = document.createElement("OPTION");
  optn.text = text;
  optn.value = value;
  selectbox.options.add(optn);
 }

thanks, Piero

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Re: [Jmol-users] (no subject)

[Robert Hanson]

Well, sort of. You can store multiple surfaces in a single JVXL file, but
right now there's no way to read them all into different frames all at once.
However, since the browser will cache the files, you might want to try that.
I haven't worked out a way to write a set of surfaces to a file, so you
would have to construct this file manually, cutting and pasting. Probably
not a solution for you. But it's not terribly difficult. The negative number
on the "35 90 Jmol voxel format" line tells how many surfaces are in the
file. Then the data are just appended:

-2 35 90 Jmol voxel format version 0.9
0.03 1318 1114 compressionRatio=416.05264
 25704 1 38 ... 34 5 35 5 35 5 36 3 38 1 25695
$x#(]>:Fd;VX_3R...
-0.03 1317 1102 compressionRatio=418.28854
 25695 2 37 3...5 5 35 5 36 3 38 1 25704
#x#%iA=FX8...

You would still have to do something like:

frame 1;isosurface "myfile.jvxl" 1
frame 2;isosurface "myfile.jvxl" 2

etc.

I know, not a great solution.

Bob





On Mon, Nov 9, 2009 at 2:06 PM, Edgar Luttmann  wrote:

> Hi,
>
> I am using JMol to display an animation with surfaces. For performance
> issues I precalculate those surface and store them as jvxl files. One sample
> animation consists of 41 frames and currently I need to load 41 jvxl
> surfaces for this to work.
>
> So I am wondering if there is a way to merge all precalculated surfaces
> into a single file and load that file within JMol.
>
> Thanks for any hints and cheers,
> Edgar
>
>
>
>
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[Jmol-users] (no subject)

[Edgar Luttmann]

Hi,

I am using JMol to display an animation with surfaces. For performance issues I 
precalculate those surface and store them as jvxl files. One sample animation 
consists of 41 frames and currently I need to load 41 jvxl surfaces for this to 
work. 

So I am wondering if there is a way to merge all precalculated surfaces into a 
single file and load that file within JMol. 

Thanks for any hints and cheers,
Edgar




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[Jmol-users] (no subject)

[Durga Bhavani Kuchibhatla]

Hello,

Iam new to jmol. Can u pls tell me how to load pdb files with file extension
.ent.Z into jmol applet. When I try to load pdb files with this extension,
the browser crashes( error: unrecognized file type) .


Please help

Thanks
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[Jmol-users] (no subject)

[Alejandro Rangel López]

i need info about how to use jmol program i've only opened the  
jmol.jar but then i dunno wut to do


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Re: [Jmol-users] (no subject)

[Fred Ziegler]

>Angel:

I figured it out after i sent  the e-mail. Thanks, Fred


>Hi Fred
>
>I understand that your problem is not specific to the electrostatic potential
>surface,  but just to the background color appearing momentarily in black.
>Since the isosurface takes some time to load, there may be a delay
>causing the black color to remain visible.
>Two things you can try (I bet that nr. 2 will be better than nr.1):
>
>1. insert a "refresh" command after "color background white", so that Jmol
>updates the display before starting to load the isosurface.
>
>2. Use jmolSetAppletColor, which prepares the applet parameters before it
>is inserted:
>
>jmolInitialize(   etc  )
>jmolSetAppletColor("white")
>jmolApplet(200,'loadetc
>
>
>
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Re: [Jmol-users] (no subject)

[Angel Herráez]

Hi Fred

I understand that your problem is not specific to the electrostatic potential 
surface,  but just to the background color appearing momentarily in black.
Since the isosurface takes some time to load, there may be a delay 
causing the black color to remain visible.
Two things you can try (I bet that nr. 2 will be better than nr.1):

1. insert a "refresh" command after "color background white", so that Jmol 
updates the display before starting to load the isosurface.

2. Use jmolSetAppletColor, which prepares the applet parameters before it 
is inserted:

jmolInitialize(   etc  )
jmolSetAppletColor("white")
jmolApplet(200,'loadetc



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[Jmol-users] (no subject)

[Fred Ziegler]

To Those in the Know:

I would like to display an electrostatic potential map with a white 
background rather than the default black.  While this code

jmolInitialize("../jmol", 
window.location.protocol == "file:");
jmolApplet(200,'background white;load 
../jmol/jvxl/methane.jvxl;moveto 1.0 { -962 -235 -141 56.81}; 
isosurface "" translucent')


works, it loads in black first.  Is there a way to load directly in 
white?  Fred ziegler

-- 

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P.O. Box 208107
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Re: [Jmol-users] (no subject)

[Egon Willighagen]

Dear Kathy,

On Mon, Feb 2, 2009 at 1:26 AM, Kathy  wrote:
> Please remove me from the mailing list.

please visit:

https://lists.sourceforge.net/lists/listinfo/jmol-users

where you can unsubscribe yourself.

Kind regards,

Egon


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[Jmol-users] (no subject)

[Kathy]

Please remove me from the mailing list.


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Re: [Jmol-users] (no subject)

[Egon Willighagen]

On Tue, Dec 2, 2008 at 5:00 AM, Kathy <[EMAIL PROTECTED]> wrote:
> Please remove me from the mailing list.  This is not what I thought it was.

You can unsubscribe at:

https://lists.sourceforge.net/lists/listinfo/jmol-users

Egon

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[Jmol-users] (no subject)

[Kathy]

Please remove me from the mailing list.  This is not what I thought it was.

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[Jmol-users] (no subject)

[David Leader]

Green links work fine on Safari 3.1 and Firefox 2 on Mac OS X 10.4.11  
and 10.5.2 for 1eve.


David

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Re: [Jmol-users] (no subject)

[Egon Willighagen]

On Dec 19, 2007 11:38 AM, Mike Miller <[EMAIL PROTECTED]> wrote:
>  Please include me in the list,

You should be subscribed now.

Egon

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[Jmol-users] (no subject)

[Mike Miller]

H,
Please include me in the list,
Mike
 
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Re: [Jmol-users] (no subject)

[Bob Hanson]

Jonathan Ouellet wrote:

> Hi,
>
>
> I would like to overlay a density map over a pdb model in Jmol so that 
> I could happily put it on the web.
>
> However, I saw that Jmol handle only gaussian cube density maps.
>
> Unfortunately, I don't have access to that expensive software (and I 
> don't really know what it is).
>
> I was wondering if there is a way to convert to .cub, or ideally, 
> insert a CCP4 or xplor density map in Jmol ?


I'd love to get CCP4 or explor density maps in Jmol.

Send me some sample files -- the PDB model, the density maps, any 
information you have about format -- and I will do it.

Bob

>
>
> cheers
>
> jo
>
>
>
>
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[Jmol-users] (no subject)

[Jonathan Ouellet]

Hi,


I would like to overlay a density map over a pdb model in Jmol so  
that I could happily put it on the web.


However, I saw that Jmol handle only gaussian cube density maps.

Unfortunately, I don't have access to that expensive software (and I  
don't really know what it is).


I was wondering if there is a way to convert to .cub, or ideally,  
insert a CCP4 or xplor density map in Jmol ?



cheers

jo


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Re: [Jmol-users] (no subject)

[Bob Hanson]

this is fixed and should show up in the next release.

Eran Hodis wrote:

>It appears that saving a state in Jmol does not save the backbone  
>setting.
>
>Is there a way I can make the state save the backbone setting, or  
>alternatively, ask Jmol "what is the backbone setting" so that my  
>code can add the backbone setting automatically to the saved state?
>
>Thank you,
>Eran Hodis
>
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Re: [Jmol-users] (no subject)

[Bob Hanson]

Eran Hodis wrote:

>It appears that saving a state in Jmol does not save the backbone  
>setting.
>
>Is there a way I can make the state save the backbone setting, or  
>alternatively, ask Jmol "what is the backbone setting" so that my  
>code can add the backbone setting automatically to the saved state?
>
>  
>
that would be a bug. I'll look into it.
   

>Thank you,
>Eran Hodis
>
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Re: [Jmol-users] (no subject)

[Bob Hanson]

Hmm. Backbone is a particularly difficult one to save in a state. The 
simple idea I tried did not work, so I will experiment some more. I 
don't have time right now to come up with a solution.

Eran Hodis wrote:

>It appears that saving a state in Jmol does not save the backbone  
>setting.
>
>Is there a way I can make the state save the backbone setting, or  
>alternatively, ask Jmol "what is the backbone setting" so that my  
>code can add the backbone setting automatically to the saved state?
>
>Thank you,
>Eran Hodis
>
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Re: [Jmol-users] (no subject)

[Bob Hanson]

Herráez Sánchez Angel wrote:

>Eran wrote:
>  
>
>>I'd like to save a state as a script in such a way that when that  
>>state-script is recalled on a Jmol applet already displaying  
>>something, that state-script will load without affecting the spin- 
>>state of the applet 
>>
>>
>
>Hello
>
>Easiest way: if the script is saved to a file, edit it and remove the spin 
>command from the state-script.
>
>  
>
won't work -- loading the file resets any spinning, and you can't .


>Otherwise, I think you can use "show spin" to read the spin state before 
>calling the state, then issue it after the script.
>  
>
that's the way to do it.

JavaScript:

var spinState = jmolEvaluate('script("show spin")'))

gets you something like:

 spinX = 0;spinY = 30;spinZ = 0;spinFps = 30;
  spin 20.0 {2.3090453 0.0 0.0} {1.3767258 1.136295 0.6437832};

which can then later be used.


or Jmol script, not JavaScript:

  spinState = script("show spin");
  script "mysavedstate.spt";
  print script(spinState);

The "print" doesn't do anything, but it allows the script now saved in 
spinState to be executed.


>I did something similar for a "Foolproof spin toggle" you can see at
>http://wiki.jmol.org:81/index.php/Recycling_Corner#.22Foolproof.22_spin_toggle
>That may give you an idea.
>
>  
>
>
>
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http://www.stolaf.edu/people/hansonr


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

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



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[Jmol-users] (no subject)

[Eran Hodis]

It appears that saving a state in Jmol does not save the backbone  
setting.

Is there a way I can make the state save the backbone setting, or  
alternatively, ask Jmol "what is the backbone setting" so that my  
code can add the backbone setting automatically to the saved state?

Thank you,
Eran Hodis

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Re: [Jmol-users] (no subject)

[Herráez Sánchez Angel]

Eran wrote:
> I'd like to save a state as a script in such a way that when that  
> state-script is recalled on a Jmol applet already displaying  
> something, that state-script will load without affecting the spin- 
> state of the applet 

Hello

Easiest way: if the script is saved to a file, edit it and remove the spin 
command from the state-script.

Otherwise, I think you can use "show spin" to read the spin state before 
calling the state, then issue it after the script.
I did something similar for a "Foolproof spin toggle" you can see at
http://wiki.jmol.org:81/index.php/Recycling_Corner#.22Foolproof.22_spin_toggle
That may give you an idea.

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[Jmol-users] (no subject)

[Eran Hodis]

Dear Jmol Users,

In addition to my question yesterday concerning the total number of  
atoms selected, I have another question I hope you can lend your  
expertise to:

I'd like to save a state as a script in such a way that when that  
state-script is recalled on a Jmol applet already displaying  
something, that state-script will load without affecting the spin- 
state of the applet -- that is, if the applet has spin on before  
loading the state-script, then spin stays on, and if spin was off  
prior to loading the state-script, then spin stays off.

Any ideas?

Best,
Eran

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[Jmol-users] (no subject)

[Benny Chain]

Does anyone know if it is possible to define a file name (for example to
save an image) as a variable , so that one can automatically move from file
to file in a looping script ? Or is there any other way to save repeated
images not in the same file during script execution ?
 
Benny Chain
 
Benjamin Chain
Department of Immunology and Molecular Pathology Windeyer Institute of
Medical Sciences UCL, 46 Cleveland St.
London W1T 4JF
Fax 00 44 20 7679 9301
 
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Re: [Jmol-users] (no subject)

[Bob Hanson]

Thanks, Craig. That's just what I needed.

Craig T Martin wrote:

> Bob,
>
>As someone else pointed out, i think, when you access the signed 
> applet, it will ask you for permission to run. A dialog will pop up 
> before Jmol fully loads. If you get that dialog, and then everything 
> after that goes smoothly, then the signed applet is working.
>
>   It will only ask you once per session. To see the request again, 
> you'll have to quit your browser and then reopen.
>
>   You can pull down a test that when run locally should automatically 
> run the trusted applet at:
>
> 
>
> Craig
>
> Craig Martin
> [EMAIL PROTECTED] 
>
>
>
> On May 3, 2007, at 11:31 AM, Bob Hanson wrote:
>
>> Craig T Martin wrote:
>>
 Message: 3
 Date: Wed, 02 May 2007 19:14:11 -0500
 From: Bob Hanson <[EMAIL PROTECTED]  
 >
 Subject: [Jmol-users] signed applets
 To: jmol-users@lists.sourceforge.net 
  
 
 Message-ID: <[EMAIL PROTECTED] 
  
 >
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 I looking for someone who is using the signed applet.
>>>
>>>
>>>
>>> Dear Bob,
>>>
>>>I use it all the time, though only for local file access, not 
>>> from one server to another.
>>>
>>>   In my usage, i have a javascript that figures out if the access is 
>>> local or to a server. If the former, then it uses the signed applet. 
>>> Thus all of my local development is with the signed applet.
>>>
>>>   However, I've had a hard time keeping up with the (fantastic) pace 
>>> of your development. The most recent version I've used is 10.9.98. 
>>> The signed applet works great with that (on a Mac, usually Safari).
>>>
>>>Did you have a specific question?
>>>
>> Yes. What should I do to test that I have the signed applet working?
>>
>>> Craig
>>>
>>> Craig Martin
>>> [EMAIL PROTECTED]  
>>> 
>>>
>>>
>>>
>>
>
>
>
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>
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Re: [Jmol-users] (no subject)

[Craig T Martin]

Bob,

   As someone else pointed out, i think, when you access the signed  
applet, it will ask you for permission to run. A dialog will pop up  
before Jmol fully loads. If you get that dialog, and then everything  
after that goes smoothly, then the signed applet is working.


  It will only ask you once per session. To see the request again,  
you'll have to quit your browser and then reopen.


  You can pull down a test that when run locally should  
automatically run the trusted applet at:




Craig

Craig Martin
[EMAIL PROTECTED]



On May 3, 2007, at 11:31 AM, Bob Hanson wrote:


Craig T Martin wrote:


Message: 3
Date: Wed, 02 May 2007 19:14:11 -0500
From: Bob Hanson <[EMAIL PROTECTED] >
Subject: [Jmol-users] signed applets
To: jmol-users@lists.sourceforge.net 
Message-ID: <[EMAIL PROTECTED] [EMAIL PROTECTED]>>

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

I looking for someone who is using the signed applet.



Dear Bob,

   I use it all the time, though only for local file access, not  
from one server to another.


  In my usage, i have a javascript that figures out if the access  
is local or to a server. If the former, then it uses the signed  
applet. Thus all of my local development is with the signed applet.


  However, I've had a hard time keeping up with the (fantastic)  
pace of your development. The most recent version I've used is  
10.9.98. The signed applet works great with that (on a Mac,  
usually Safari).


   Did you have a specific question?


Yes. What should I do to test that I have the signed applet working?


Craig

Craig Martin
[EMAIL PROTECTED] 







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[Jmol-users] (no subject)

[Craig T Martin]

Message: 3
Date: Wed, 02 May 2007 19:14:11 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: [Jmol-users] signed applets
To: jmol-users@lists.sourceforge.net
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

I looking for someone who is using the signed applet.


Dear Bob,

   I use it all the time, though only for local file access, not  
from one server to another.


  In my usage, i have a javascript that figures out if the access is  
local or to a server. If the former, then it uses the signed applet.  
Thus all of my local development is with the signed applet.


  However, I've had a hard time keeping up with the (fantastic) pace  
of your development. The most recent version I've used is 10.9.98.  
The signed applet works great with that (on a Mac, usually Safari).


   Did you have a specific question?

Craig

Craig Martin
[EMAIL PROTECTED]



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Re: [Jmol-users] (no subject)

[Bob Hanson]

In 11.1.x we are recommending going to a simpler method of naming models 
in multiple file mode:

Files have each one model:

1.1, 2.1, 3.1, 

Files have more than one model:

1.1, 1.2, 1.3, ... 2.1, 2.2, 2.3 etc.

Then, in analogy to

model 0

for displaying all models, now we have:

model 1.0   # all models in File 1

The original idea of 1001 2001 3001 still is implemented, but this is 
better.
Also, in 11.1.x I fixed it so that

model 1
model 2

etc. works as well, as long as the files really only have one model each.
That's because "model 1" is the same as "model 1.0" -- "all models in 
file 1".

So if you say

model 1

or

model 1.0

that's the same -- all models in file 1.

I think this works reasonably intuitively.

Bob






Bob



Angel Herraez wrote:

>Hi Harris
>
>Although others had posted more detailed solutions to your question, 
>I think the problem you had with
>
>  
>
>>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;');
>>It shows 1BZ8 structure. But if i do : 
>>
>>
>>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;');
>>It shows nothing.. .is it normal ? 
>>
>>
>
>
>is that, when several files are loaded, they are assigned frame/model 
>numbers 1001, 2001, not 1, 2. So, in your examples:
>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select 
>*/1001;');  # first model in 1BZ8.pdb
>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select 
>*/2001;');  # first model in 1C26.pdb
>
>The new syntax in Jmol 11.1.x allows to use the more clear "file 1", 
>"file 2" and "1.1", "1.2", "2.1"   identifiers, which have already 
>been recommended by others.
>
>HTH
>
>
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Re: [Jmol-users] (no subject)

[Angel Herraez]

Hi Harris

Although others had posted more detailed solutions to your question, 
I think the problem you had with

> jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;');
> It shows 1BZ8 structure. But if i do : 
> 
> 
> jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;');
> It shows nothing.. .is it normal ? 


is that, when several files are loaded, they are assigned frame/model 
numbers 1001, 2001, not 1, 2. So, in your examples:
jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select 
*/1001;');  # first model in 1BZ8.pdb
jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select 
*/2001;');  # first model in 1C26.pdb

The new syntax in Jmol 11.1.x allows to use the more clear "file 1", 
"file 2" and "1.1", "1.2", "2.1"   identifiers, which have already 
been recommended by others.

HTH


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Re: [Jmol-users] (no subject)

[Frieda Reichsman]

oops - I misspoke --

I said:



you need to insert the command
file 0
which makes all the files you loaded "displayable" (but not displayed)



BUT I was incorrect.
"file 0" actually does display all the files loaded.

So instead say

so say:
jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; file 0;  
display file=2;');


the command
display file=2
is what displays ONLY file 2.

Below is a "reprint" of a complete explanation that Bob H wrote to  
the list  yesterday (in response to my questions).


Frieda

  reprint  
Bob said:


The logic is supposed to be:

"display x"  hides all atoms except x.
"hide x" displays all atoms except x.

To this we add:

display xxx  # display ONLY x
hide not xxx# same thing!

display not xxx  # display everything but x
hide xxx   # same thing!

display hidden # toggle shown for unshown
hide displayed # same thing!

display displayed and not xxx  # remove xxx from the display --- what
you want here
hide hidden or xxx # same thing!

display displayed or xxx  # add x to the display --- also what you  
want

hide hidden and not xxx   # add x to the display

So just don't use "hide" if it confuses you. It is never necessary.
Thinking in terms of what is displayed gets you anything you want. The
key for this situation is to use "displayed" as part of that  
checkbox item.


[x] file 1: [x]"display displayed or file=1"  [ ] "display  
displayed

and not file=1"
[x] file 2 :[x]"display displayed or file=2"  [ ] "display  
displayed

and not file=2"
[x] file 3 :[x]"display displayed or file=3"  [ ] "display  
displayed

and not file=3"

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Re: [Jmol-users] (no subject)

[Frieda Reichsman]

you need to insert the command
file 0
which makes all the files you loaded "displayable" (but not displayed)

so say
jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; file 0; select  
*/2; spacefill on;');


the last command is just to actually render the structure in a style,  
choose whatever rendering you like.


Also, the reason that
select */1
worked was simply that when you load multiple files, only the first  
one shows up by default.


Frieda




On Mar 1, 2007, at 9:40 AM, <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> wrote:



ok thank you...


Now when I do :


jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;');

It shows 1BZ8 structure. But if i do :

jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;');


It shows nothing.. .is it normal ?


Egon Willighagen a écrit :

On Thursday 01 March 2007 15:28:35 [EMAIL PROTECTED] wrote:
The last method i tried is :

print qq{



};

Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb'
'1C26.pdb'; select */2;");

You still need to apply what Angel mentioned: switch the " and ' in  
the load

command. So:

print qq{



};

E.



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///

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com

///


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[Jmol-users] (no subject)

[harris]

ok thank you... Now when I do :  jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;');It shows 1BZ8 structure. But if i do : jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); It shows nothing.. .is it normal ? Egon Willighagen a écrit :
  On Thursday 01 March 2007 15:28:35 [EMAIL PROTECTED] wrote:
  The last method i tried is :print qq{        
  jmolInitialize("../softs/jmol-10.2.0");
    jmolApplet(300, "load 'fileset'
'../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;");
        };Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb''1C26.pdb'; select */2;");
  You still need to apply what Angel mentioned: switch the " and ' in the load command. So:print qq{
  jmolInitialize("../softs/jmol-10.2.0");
jmolApplet(300, 'load "fileset"
"../pdb_structures/1BZ8.pdb" "../pdb_structures/1C26.pdb"; select */1;');
};E.

 


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Re: [Jmol-users] (no subject)

[Egon Willighagen]

On Thursday 01 March 2007 15:28:35 [EMAIL PROTECTED] wrote:
> The last method i tried is :
>
> print qq{
>     
>     
>   jmolInitialize("../softs/jmol-10.2.0");
>     jmolApplet(300, "load 'fileset'
> '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;");
> 
>     
>     };
>
> Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb'
> '1C26.pdb'; select */2;");

You still need to apply what Angel mentioned: switch the " and ' in the load 
command. So:

print qq{


  jmolInitialize("../softs/jmol-10.2.0");
jmolApplet(300, 'load "fileset"
"../pdb_structures/1BZ8.pdb" "../pdb_structures/1C26.pdb"; select */1;');


};

E.

-- 
CUBIC
blog: http://chem-bla-ics.blogspot.com/

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[Jmol-users] (no subject)

[harris]

thanx all for your help but I tried all the possibilities and it does not work...The last method i tried is :print qq{        
  jmolInitialize("../softs/jmol-10.2.0");
    jmolApplet(300, "load 'fileset' '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;");
            };Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb' '1C26.pdb'; select */2;");Should the applet show anything or not ?ThanxHarris 


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Re: [Jmol-users] (no subject)

[Rolf Huehne]

Harris Procopiou wrote:
> I try to load multiple files but i can't... I 'm working with perl :
>
> print "
>
> 
> jmolInitialize("Jmol.js");
> jmolApplet(300, "load "fileset" "1BZ8.pdb" 
> "1C26.pdb"; select */2; color red;");
> 
> ";
>
> The problem is quotes... how can i do this ?
>
> I tried :
>
> print "
>
> 
> jmolInitialize("Jmol.js");
> jmolApplet(300, "load 'fileset' '1BZ8.pdb' 
> '1C26.pdb'; select */2; color red;");
> 
> ";
>
> But it does not work too. And :
>
> print "
>
> 
> jmolInitialize("Jmol.js");
> jmolApplet(300, load "fileset" "1BZ8.pdb" 
> "1C26.pdb"; select */2; color red;);
> 
> ";
>
> The same..
>
>   
 Hi Harris,

since you mentioned perl as the script language you are using to create
the HTML code I guess your question refers to the syntax errors you will
get in perl if you try the above 'print' commands.
There are two methods in perl to solve this problem. The first one is to
'escape' the double quotes inside the 'print' statement with a
backslash,e.g.:

 print "jmolApplet(300, \"load 'fileset' '1BZ8.pdb' '1C26.pdb'\");";

The disadvantage of this method is that the text is less good readable
and that you have to change the HTML code you might have tested in a
plain HTML text before you started to integrate it into your perl script.
Therefore I prefer the second method:  using the general quoting
operator 'qq'.
The above example could look like this:

print qq{jmolApplet(300, "load 'fileset' '1BZ8.pdb' '1C26.pdb");};

You can replace the brace ('{') behind the 'qq'  by any other
non-alphanumeric character. Then the end brace ('}') must also be
replaced by the same character (or the corresponding closing bracket
character if you use '(' or '[').
In my work the brace has proven to work in most cases for HTML code.

Regards,
Rolf



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Re: [Jmol-users] (no subject)

[Egon Willighagen]

Hi Harris,

On Thursday 01 March 2007 13:15:16 Harris Procopiou wrote:
> I try to load multiple files but i can't... I 'm working with perl :
>
> print "
>
> 
> jmolInitialize("Jmol.js");
> jmolApplet(300, "load "fileset" "1BZ8.pdb"
> "1C26.pdb"; select */2; color red;");
> 
> ";

In Perl you can escape the quotes with \"... so try this:

print "
   

jmolInitialize(\"Jmol.js\");
jmolApplet(300, 'load \"fileset\" \"1BZ8.pdb\"
\"1C26.pdb\"; select */2; color red;');

";

Egon

-- 
CUBIC
blog: http://chem-bla-ics.blogspot.com/

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Re: [Jmol-users] (no subject)

[Angel Herraez]

Hello Harris 

Yes, it seems a quotes problem.

First, try this: Jmol requires double quotes for load, so you should 
use single quotes for the javascript:


 
 jmolInitialize('.');
 jmolApplet(300, 'load "fileset" 
"1BZ8.pdb"  "1C26.pdb"; select */2; color red;');
 
 
 

However, since you have a more external set of double quotes for your 
"print", it may not work. 

I think I read about the use of ", but right now I canot find 
it. If I do, I will post again.
If you want to try, it could be (I haven't checked):


 
 jmolInitialize('.');
 jmolApplet(300, 'load 
"fileset" "1BZ8.pdb"  "1C26.pdb"; 
select */2; color red;');
 
 
 


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Re: [Jmol-users] (no subject)

[Frieda Reichsman]

Thanks, Bob, I never seem to remember the /model syntax, and the last  
solution is great - so simple.

Frieda

On Feb 28, 2007, at 11:48 PM, Bob Hanson wrote:


Frieda Reichsman wrote:


Say I have 3 files loaded but my set of labels should appear on only
one of them. I also want to be able to turn on and off the display of
the three proteins at will.

Is there an easy way to select a series of single atoms for labeling
and have the label apply only to one file?

Or is the only way to do this to repeat "select file=1 and ..." over
and over, like so:

select file=1 and 263.n
label helix 1


If it's one model per file, you can just use the old syntax:

select 263.n/1; label helix1

Certainly you need only the number of select/label combinations as you
have distinct labels, but other than that, yes, you need to specify  
the

atom and model number to get the label on just that atom.


In other words is there some way to say, "the following selections
apply ONLY to file =1" (and then also end it in some way)?


Well, you could do:

select 263.n; label helix1
select 283.n; label helix2
...
select file != 1
labels off

That is, just put all the labels in, but then in the end turn the
unwanted ones off.

Bob



///


Frieda Reichsman, PhD

Molecules in Motion

Interactive Molecular Structures

http://www.moleculesinmotion.com


///






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///

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com

///


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Re: [Jmol-users] (no subject)

[Frieda Reichsman]

Hi Harris,


jmolInitialize("Jmol.js");


is incorrect - in the parenthesis should be the path to the Jmol  
applet. If the applet is in the same directory, use simple a single  
dot (.).


Jmol.js must be referred to in the header, like this:
script>

Frieda

On Mar 1, 2007, at 7:15 AM, Harris Procopiou wrote:

I try to load multiple files but i can't... I 'm working with perl :

print "