Re: [Jmol-users] "polyhedra bonds opaque" broken

[Robert Hanson]

please enter as a request for a bug fix; in the mean time, please use
"color polyhedra opaque" :)


On Wed, 2 Jan 2008 19:05:49 +0100, Paul Pillot
<[EMAIL PROTECTED]> wrote:
> Happy new year to all Jmolers !
> I think there is something broken in respect with polyhedra
> translucency :
> "polyhedra bonds (selected) translucent" works fine
> "polyhedra bonds (selected) opaque" does not restore the default view
> whereas "color polyhedra opaque" does...
> Paul
> 
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Re: [Jmol-users] something broken in Jmol states (?)

[Robert Hanson]

looks like a missing semicolon after "color selectionHalos none"
If you can fix that manually for now, that will make it work. 

[[Egon, can you fix this? It's in org/jmol/shapes/Halos.Java

   62  public String getShapeState() {
   63 return super.getShapeState()
   64 + (colixSelection == Graphics3D.USE_PALETTE ? ""
   65 : colixSelection == Graphics3D.INHERIT_ALL ? "  color
SelectionHalos NONE"
   66 : getColorCommand("selectionHalos", colixSelection) +
";\n");

line 65 should read:

   65 : colixSelection == Graphics3D.INHERIT_ALL ? "  color
SelectionHalos NONE;\n"

Bob

On Wed, 2 Jan 2008 19:08:30 +0100, Paul Pillot
<[EMAIL PROTECTED]> wrote:
> I got this message runing a state from the applet with Jmol 11.3.63 :
> script ERROR: bad argument count | line 12 command 11 of function
> _setmodelstate file null: | color selectionHalos none select ({1189})
> << | line 6 command 6 of function _setstate file null: | >>
> _setmodelstate << | line 513 command 1 of file null: | >>
> _setstate <<
> the file is loaded but the complete view is not restored...
> Paul


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Re: [Jmol-users] minimum Jmol download

[Robert Hanson]

On Wed, 2 Jan 2008 21:02:59 -0500, Frieda Reichsman <[EMAIL PROTECTED]>
wrote:
> Bob, two part question:
> 
> 1, Which component files of Jmol will download when a page has an
> applet displaying one structure (DNA only), in wireframe only, with
> NO buttons or other controls? (Assuming I am using the 'components'
> version of Jmol jar files).

[ x  ] JmolApplet0_Core.jar   30-Dec-2007 23:22  157K  
[ x  ] JmolApplet0_Jars.jar   30-Dec-2007 23:23   55K  
[   ] JmolApplet0_Jvxl.jar   30-Dec-2007 23:23   79K  
[ x  ] JmolApplet0_Main.jar   30-Dec-2007 23:23   36K  
[ x  ] JmolApplet0_Popup.jar  30-Dec-2007 23:23   30K  
[   ] JmolApplet0_Quantum.jar30-Dec-2007 23:23  8.5K  
[ x  ] JmolApplet0_ReadersCifPdb.jar  30-Dec-2007 23:23   15K  
[ x  ] JmolApplet0_ReadersMolXyz.jar  30-Dec-2007 23:23  4.5K  
[   ] JmolApplet0_ReadersMore.jar30-Dec-2007 23:23   65K  
[   ] JmolApplet0_ReadersXml.jar 30-Dec-2007 23:23   22K  
[ x  ] JmolApplet0_ShapeBio.jar   30-Dec-2007 23:23   50K  
[   ] JmolApplet0_ShapeSpecial.jar   30-Dec-2007 23:23   54K  
[   ] JmolApplet0_Smiles.jar 30-Dec-2007 23:23  7.8K  
[ x  ] JmolApplet0_Viewer.jar 30-Dec-2007 23:23  384K  
[ x  ] JmolApplet0_i18n.jar   30-Dec-2007 23:23  127K  

I think. 

> 
> 2, If there is a jvxl surface, would the only additional component be
> the JmolApplet0_Jvxl.jar file?

also "ShapeSpecial"

> 
> I'd like to be able to compare the file sizes for a user downloading
> an applet with a simple rotating structure vs. downloading various
> sizes of animated gifs.

great.

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


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Re: [Jmol-users] Small buglet in saving graphics state (Jmol 11.4)

[Robert Hanson]

thank you - please enter as an official request for a bug fix. 
Perhaps Egon can find that code in SelectionManager.java and fix it for us.



On Fri, 4 Jan 2008 15:50:11 +, Brian McMahon <[EMAIL PROTECTED]> wrote:
> Hello
> 
> If one invokes the Jmol console (at least in 11.4RC1) and clicks the
> "State" button, among the contents one finds
> 
>function _setSelectionState();
> select ({0:48});
> set hideNotSelected false;
>end function
> 
> Note that the final "end function" does not have a closing semicolon.
> This is legitimate; but if one then copies and pastes the graphics state
> as an inline argument to jmolApplet() one must collapse the state
> description into a single line, when the end function is no longer a
> properly terminated statement.
> 
> For now I can workaround this by massaging the state as it is collapsed
> into
> a single line, but it would be good if this minor flaw were corrected in
> future releases, and each statement were terminated with a semicolon.
> 
> Cheers
> Brian
> _
> Brian McMahon   tel: +44 1244 342878
> Research and Development Officerfax: +44 1244 314888
> International Union of Crystallographye-mail:  [EMAIL PROTECTED]
> 5 Abbey Square, Chester CH1 2HU, England
> 
> -
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
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Re: [Jmol-users] Interactive 3D Organic Reaction Mechanisms

[Nick Greeves]

Hi Henry,
Thanks for your kind comments. I see what you mean about the  
"antarafacial" nature of the ozonolysis. I had not intended to imply  
any antara/suprafacial aspect to the 3D arrows but like you I think  
this could be used specifically to stress this important aspect  
perhaps by using a different colour or weight to the arrow (both can  
be controlled). [and then another colored arrow for conrotatory and  
disrotatory!]


I've done some more pericyclic reactions but have more to do before  
they are ready.


I was aiming for an "atom-specific" curly arrow passing through the  
atom that reacts - Organic Chemistry Clayden et al p 124


As with so much in Jmol, creating the 3D curly arrows is  
straightforward.

http://chemapps.stolaf.edu/jmol/docs/examples-11/draw.htm
curves, arrows, OFFSET, set picking DRAW, and show DRAW - you can  
experiment here


The process involves drawing any arrow, set picking DRAW,  dragging  
the three points of the 3D curve to the desired positions (alt or  
shift) and then issuing show DRAW - the relevant command can then be  
copied into the load command from Console


e.g.
  draw arrow1 ARROW {-2.5876317 -0.14727443 -0.4237} {-0.9625803  
2.3060563 -0.962} {0.59135246 -0.35723114 2.9140291};

  draw arrow1 fill noMesh noDots notFrontOnly fullylit;
  color draw opaque [xffa500];


All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel: +44 (0)151-794-3506 (3500 secretary)


On 4 Jan 2008, at 19:57, [EMAIL PROTECTED] wrote:



Message: 6
Date: Fri, 4 Jan 2008 19:56:12 +
From: "Rzepa, Henry" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Interactive 3D Organic Reaction Mechanisms
To: jmol-users@lists.sourceforge.net
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"


Dear Jmol users,
I would like to draw to your attention a new site I have developed  
using Jmol (with much help from many of you, especially Bob) to  
depict
interactive 3D animations for some of the most important organic  
reactions covered during an undergraduate degree with supporting  
information on reactivity.


http://osxs.ch.liv.ac.uk/~ng/external/

If you are a student or teacher of Organic chemistry, I hope you  
will find it interesting and useful. It is intended to supplement  
existing textbooks and lectures and I use it regularly projected -  
Jmol makes it look great!



What a splendid site Nick.

I have one question.  I have for years taught eg pericyclic  
mechanisms, where
I drum home to the students that pushed arrows have three   
dimensions.  Thus suprafacial,
antarafacial, etc etc.   Its a specific case of the more general  
stereoelectronic theory

of chemistry.

This  3D nature is a little tricky to display.  for example,  I am  
looking at
the  1,3 dipolar cycloaddtion for ozonolysis, where unless  I am  
mistaken, the arrows could
be taken to indicate  antarafacial on the carbonyl and antarafacial  
on the  1,3 dipole.


Whilst this is actually "allowed", no 4a + 2a  cycloaddition is  
actually known.
I must confess to being both impressed and baffled as to how the  
arrows
were generated,  but is it possible to show the suprafacial/ 
antarafaciality with
greater precision, ie  true  3D arrows (after all,  Jmol is the only  
tool for arrow

pushing  I have ever seen which is capable of doing this!)

Generally, how does one go about authoring this?  How long would it  
take to eg

position  one arrow in a starting set of  3D coordinates?
--

Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED] 
 (iChat)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College  
London, SW7  2AZ, UK.


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Re: [Jmol-users] Interactive 3D Organic Reaction Mechanisms

[Rzepa, Henry]

>Dear Jmol users,
>I would like to draw to your attention a new site I have developed using Jmol 
>(with much help from many of you, especially Bob) to depict
>interactive 3D animations for some of the most important organic reactions 
>covered during an undergraduate degree with supporting information on 
>reactivity.
>
>http://osxs.ch.liv.ac.uk/~ng/external/
>
>If you are a student or teacher of Organic chemistry, I hope you will find it 
>interesting and useful. It is intended to supplement existing textbooks and 
>lectures and I use it regularly projected - Jmol makes it look great!


What a splendid site Nick.

I have one question.  I have for years taught eg pericyclic mechanisms, where
I drum home to the students that pushed arrows have three  dimensions.  Thus 
suprafacial,
antarafacial, etc etc.   Its a specific case of the more general 
stereoelectronic theory
of chemistry. 

This  3D nature is a little tricky to display.  for example,  I am looking at
the  1,3 dipolar cycloaddtion for ozonolysis, where unless  I am mistaken, the 
arrows could
be taken to indicate  antarafacial on the carbonyl and antarafacial on the  1,3 
dipole.

Whilst this is actually "allowed", no 4a + 2a  cycloaddition is actually known.
I must confess to being both impressed and baffled as to how the arrows
were generated,  but is it possible to show the suprafacial/antarafaciality with
greater precision, ie  true  3D arrows (after all,  Jmol is the only tool for 
arrow
pushing  I have ever seen which is capable of doing this!)

Generally, how does one go about authoring this?  How long would it take to eg
position  one arrow in a starting set of  3D coordinates?
-- 

Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED] 
(iChat)
 http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7  
2AZ, UK.

(Voracious anti-spam filter in operation for received email.
If expected reply not received, please phone/fax).


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[Jmol-users] Small buglet in saving graphics state (Jmol 11.4)

[Brian McMahon]

Hello

If one invokes the Jmol console (at least in 11.4RC1) and clicks the
"State" button, among the contents one finds

   function _setSelectionState();
select ({0:48});
set hideNotSelected false;
   end function

Note that the final "end function" does not have a closing semicolon.
This is legitimate; but if one then copies and pastes the graphics state
as an inline argument to jmolApplet() one must collapse the state
description into a single line, when the end function is no longer a
properly terminated statement.

For now I can workaround this by massaging the state as it is collapsed into
a single line, but it would be good if this minor flaw were corrected in
future releases, and each statement were terminated with a semicolon.

Cheers
Brian
_
Brian McMahon   tel: +44 1244 342878
Research and Development Officerfax: +44 1244 314888
International Union of Crystallographye-mail:  [EMAIL PROTECTED]
5 Abbey Square, Chester CH1 2HU, England

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Re: [Jmol-users] Continuous Symmetry Measures - A new website

[Herráez Sánchez Angel]

Inbal, I suggest that you add your site to the list existing at Jmol Wiki

http://wiki.jmol.org:81/index.php/Websites_Using_Jmol 

<>-
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Re: [Jmol-users] applet size and set pickCallback

[Herráez Sánchez Angel]

Steve, percent-sized div should work, even in Ohio, but there may be browser 
issues limitng it, if I remember correctly. Check out the code of my templates
http://biomodel.uah.es/Jmol/resizable/
I had to set html {height:100%} and body {height:100%} for this to work 
properly in all browsers; maybe that helps you.

~~~
Steven R. Spilatro  wrote:

As you suggested, when sizing the applet in Firefox by percent or 
fractions, the applet must be within a fully qualified div; however, 
the div height must be set to a px value; setting height to a percent 
value does not work -- at least in Ohio.
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