Re: [Jmol-users] Nested quotes problem

[Greeves, Nick <ngreeves@li...>]

Thanks Mike,
I'll try that. I found http://www.c-point.com/javascript_tutorial/special_characters.htm which is similar.

I think I may also be having problems with the symmetry of the molecules.

defaultOrientationMatrix = [
  [-0.0100188255 0.3289951 0.9442785]
  [0.78089386 -0.5872656 0.21289393]
  [0.62458336 0.73951423 -0.25102657] ]
Time for openFile(model/ltf/SF5.spardir): 31 ms
reading 6 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
defaultOrientationQuaternion = {0.6760683 0.41042045 0.5801418 0.19473635}
Use "set autoLoadOrientation TRUE" before loading or "restore orientation DEFAULT" after loading to view this orientation.
Default Van der Waals type for model set to Babel
6 atoms created
ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation
1 atoms selected
QueueThread0_59 exception java.lang.NullPointerException
java.lang.NullPointerException
at org.jmol.modelset.AtomCollection.getHybridizationAndAxes(Unknown Source)
at org.jmol.viewer.Viewer.getHybridizationAndAxes(Unknown Source)
at org.jmol.shapesurface.LcaoCartoon.createLcaoCartoon(Unknown Source)
at org.jmol.shapesurface.LcaoCartoon.createLcaoCartoon(Unknown Source)
at org.jmol.shapesurface.LcaoCartoon.setProperty(Unknown Source)
at org.jmol.viewer.ShapeManager.setShapePropertyBs(Unknown Source)
at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source)
at org.jmol.script.ScriptEvaluator.lcaoCartoon(Unknown Source)
at org.jmol.script.ScriptEvaluator.processShapeCommand(Unknown Source)
at org.jmol.script.ScriptEvaluator.commandLoop(Unknown Source)
at org.jmol.script.ScriptEvaluator.dispatchCommands(Unknown Source)
at org.jmol.script.ScriptEvaluator.executeCommands(Unknown Source)
at org.jmol.script.ScriptEvaluator.startEval(Unknown Source)
at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
at org.jmol.viewer.ScriptManager.evalStringWaitStatusQueued(Unknown Source)
at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Unknown Source)
at org.jmol.thread.ScriptQueueThread.runNextScript(Unknown Source)
at org.jmol.thread.ScriptQueueThread.run1(Unknown Source)
at org.jmol.thread.JmolThread.run(Unknown Source)

All the best
Nick
--
3D Organic Animations     http://www.chemtube3d.com
Tel:             +44 (0)151-794-3506 (3500 secretary)



On 9 Mar 2013, at 17:33, <jmol-users-request@...<mailto:jmol-users-request@...>>
 wrote:

Message: 3
Date: Sat, 9 Mar 2013 11:32:57 -0600
From: Michael Evans <evans23@...<mailto:evans23@...>>
Subject: Re: [Jmol-users] Nested quotes problem
To: "jmol-users@...<mailto:jmol-users@...>"
<jmol-users@...<mailto:jmol-users@...>>
Message-ID:
<CAPVVrdYAmNwpnLZxN4iBTjDzZa6fzehGcxiiN2ezymRG9CoPbw@...<mailto:CAPVVrdYAmNwpnLZxN4iBTjDzZa6fzehGcxiiN2ezymRG9CoPbw@...>>
Content-Type: text/plain; charset="iso-8859-1"

Nick,
Try \' rather than " around sp2a. That worked for me (I was working on
something similar in JSmol yesterday).

Cheers, Mike

On Saturday, March 9, 2013, Greeves, Nick wrote:

Hi All,
I am trying to use lcaoCartoon within a hot spot image map.

The HTML looks like this
 <map name="Map" id="Map"><area shape="rect" coords="9,1,328,344"
href="javascript:jmolScript('load model/ltf/SF5.spardir;moveto 1.0 { -512
700 -499 116.04};select (sulfur);lcaoCartoon delete create "sp2a";')"
alt="SF4" />

This does nothing when clicked. In contrast the same command operating
on SF5.spardir in Jmol.jar

select (sulfur);lcaocartoon delete create "sp2a";

works fine.

I suspect this is a problem with nested quotes. Is the " after create
being interpreted as the end of the href command?

So the question is, are there any other types of quote I can use or is
there another way of doing it?


      Best regards
Nick
--
Nick Greeves                            via OS X Mail
Director of Teaching and Learning
Department of Chemistry
University of Liverpool
Donnan and Robert Robinson Laboratories

Crown Street, LIVERPOOL L69 7ZD U.K.
Email address:    ngreeves@...<mailto:ngreeves@...> <javascript:_e({}, 'cvml',
'ngreeves@...<mailto:ngreeves@...>');>
WWW Pages:    http://www.chemtube3d.com<http://www.chemtube3d.com/>;
Tel:            +44 (0)151-794-3506 (3500 secretary)
Dept Fax:   +44 (0)151-794-3588










--

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign

Re: [Jmol-users] Console Question

[Angel Herráez <angel.herraez@ua...>]

Otis, have you tried
  show PDBHEADER
?

Re: [Jmol-users] Nested quotes problem

[Michael Evans <evans23@il...>]

Nick,
Try \' rather than " around sp2a. That worked for me (I was working on
something similar in JSmol yesterday).

Cheers, Mike

On Saturday, March 9, 2013, Greeves, Nick wrote:

>  Hi All,
> I am trying to use lcaoCartoon within a hot spot image map.
>
>  The HTML looks like this
>   <map name="Map" id="Map"><area shape="rect" coords="9,1,328,344"
> href="javascript:jmolScript('load model/ltf/SF5.spardir;moveto 1.0 { -512
> 700 -499 116.04};select (sulfur);lcaoCartoon delete create "sp2a";')"
> alt="SF4" />
>
>  This does nothing when clicked. In contrast the same command operating
> on SF5.spardir in Jmol.jar
>
>  select (sulfur);lcaocartoon delete create "sp2a";
>
>  works fine.
>
>  I suspect this is a problem with nested quotes. Is the " after create
> being interpreted as the end of the href command?
>
>  So the question is, are there any other types of quote I can use or is
> there another way of doing it?
>
>
>        Best regards
>  Nick
>  --
>  Nick Greeves                            via OS X Mail
>  Director of Teaching and Learning
>  Department of Chemistry
>  University of Liverpool
>  Donnan and Robert Robinson Laboratories
>
>  Crown Street, LIVERPOOL L69 7ZD U.K.
>  Email address:    ngreeves@... <javascript:_e({}, 'cvml',
> 'ngreeves@...');>
>  WWW Pages:    http://www.chemtube3d.com
>  Tel:            +44 (0)151-794-3506 (3500 secretary)
>  Dept Fax:   +44 (0)151-794-3588
>
>
>
>
>
>
>
>
>

-- 

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign

[Jmol-users] Nested quotes problem

[Greeves, Nick <ngreeves@li...>]

Hi All,
I am trying to use lcaoCartoon within a hot spot image map.

The HTML looks like this
  <map name="Map" id="Map"><area shape="rect" coords="9,1,328,344" href="javascript:jmolScript('load model/ltf/SF5.spardir;moveto 1.0 { -512 700 -499 116.04};select (sulfur);lcaoCartoon delete create "sp2a";')" alt="SF4" />

This does nothing when clicked. In contrast the same command operating on SF5.spardir in Jmol.jar

select (sulfur);lcaocartoon delete create "sp2a";

works fine.

I suspect this is a problem with nested quotes. Is the " after create being interpreted as the end of the href command?

So the question is, are there any other types of quote I can use or is there another way of doing it?


Best regards
Nick
--
Nick Greeves                            via OS X Mail
Director of Teaching and Learning
Department of Chemistry
University of Liverpool
Donnan and Robert Robinson Laboratories
Crown Street, LIVERPOOL L69 7ZD U.K.
Email address:    ngreeves@...<mailto:ngreeves@...>
WWW Pages:    http://www.chemtube3d.com
Tel:            +44 (0)151-794-3506 (3500 secretary)
Dept Fax:   +44 (0)151-794-3588

Re: [Jmol-users] Console Question

[Otis Rothenberger <osrothen@ch...>]

Bob,

I was working on this in response to this request from a biochemist colleague:

"It helps a lot with pdb files if you can read what they contain. It allows you to know what kind of model you are looking at (NMR, crystallographic, theoretical [rare, from some kind of modeling], to read warnings about interpretation of the model (some residues disordered and not included), and to see easily if there are HETATM groups, ions, or oddities (nonstandard residues) in the model. Some of these things are hard to discern from the default model that any such program presents."

So display while using the model kit is the objective. From his comments, the header may suffice. Either way, I'm now thinking about getting it with a message callback and putting it in what I'm now calling your Scratchpad - i.e. setInfo showInfo.

Otis

--
Otis Rothenberger
otis@...
http://chemagic.com

On Mar 8, 2013, at 1:34 PM, Robert Hanson wrote:

> 
> 
> On Fri, Mar 8, 2013 at 10:52 AM, Otis Rothenberger <osrothen@...> wrote:
> Bob,
> 
> I can't get to the search box on your page because of the immovable console. On my page with my iPad calling the alert after displaying the console results in:
> 
> function (a) {a ? this.container.show();this.container.hide();this.dragBind(a);}
> 
> This was in response to:
> 
> alert(Jmol.Console.buttons['jmolApplet0_console'].setVisible)
> 
> I follow the conditional above - not sure about this dragBind(a).
> 
> JSmol models can be touch dragged on an iPad. I'm not sure about CSS containers, however.
> 
> My ultimate objective here was that a loaded pdb file is easiest to grab by placing it in the console. That part works on the iPad, but the subsequent iPad is not responsive. You can, however, copy the pdb.
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> otis@...
> http://chemagic.com
> 
> 
> 
>