Re: [Jmol-users] Jmol 14.13.1

[Dean Johnston]

Pshemak, Otis and Bob,

Glad that I could provide something to the list. I have to admit that I set
that page up long enough ago that I can't recall exactly how I figured it
out. But it still works and it's useful.

Dean

On Mon, Apr 10, 2017 at 3:09 PM, Robert Hanson <hans...@stolaf.edu> wrote:

> OK, I know how I my comparison method violated the general contract. Very
> surprised this ever worked!
>
> On Mon, Apr 10, 2017 at 1:37 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Pshemak,
>>
>> Gotta love this error message:
>>
>> java.lang.IllegalArgumentException: Comparison method violates its
>> general contract!
>>
>> I'll check on this.
>>
>> Bob
>>
>>
>> On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>>
>>> Otis and Dean,,
>>>
>>> Thanks for the explanation. I was indeed able to find the whole command
>>> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
>>> *) * in the documentation (in the "cpk" example of lcaoCartoons).
>>>
>>> I think I understand it better now. The "spacefill" spheres are replaced
>>> with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell"
>>> as slabbing planes.
>>>
>>> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in
>>> the center of the cell and one Na+  in the corner (which is properly
>>> CAP-ed).
>>>
>>> However when I load {1 1 1} cell to get all ions within the cell, the
>>> Jmol (desktop Java app) freezes. I tried the newest version (14.13.1) an an
>>> older one (14.8.0) with the same results.
>>>
>>> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which
>>> show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell
>>> "cpk";spacefill off"  froze Jmol as well.
>>>
>>> Any suggestions?
>>>
>>> Thanks for your help.
>>>
>>> PM
>>>
>>>
>>>
>>> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>>>
>>> Pshemak,
>>>
>>> The CAP part is discussed here:
>>>
>>> https://chemapps.stolaf.edu/jmol/docs/index.htm?=
>>> 1=14.6#isosurface
>>>
>>> Scroll down until you see CAP listing.
>>>
>>> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>>>
>>> Dean, the main reason I'm jumping in here is the display unitcell
>>> command. Is that a legal Jmol Script command? After loading a CIF file, I
>>> thought that you had to do something like this to get the unit cell:
>>>
>>> save orientation; load "" {444 666 1}; set displayCellParameters
>>> false;restore orientation; unitcell on; display cell=555; center visible;
>>> zoom 200;
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.org
>>> http://chemagic.org
>>>
>>> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>>>
>>> Thank you Dean,
>>>
>>> I do not understand the
>>>
>>> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;
>>>
>>>
>>> part of the command. Is it documented in https://chemapps.stolaf.edu
>>> /jmol/docs/  ?
>>>
>>> Thanks,
>>>
>>> PM
>>>
>>>
>>> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>>>
>>> Yes - I have an example at: http://crystals.otterbein.
>>> edu/packing/index.html
>>>
>>> Pick structure from the left menu and then click the “Show Contents of
>>> One Unit Cell”. Works beautifully!
>>>
>>> The commands are:
>>> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP
>>> unitcell 'cpk'; spacefill 1%;
>>>
>>> Dean Johnston
>>>
>>> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
>>>
>>>
>>> Can the "slab" command be used to produce presentations equivalent to
>>> the image linked below?
>>>
>>> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/F
>>> ile:CCC_crystal_cell_(opaque).svg
>>>
>>> If so, any suggestions on how to do that would be appreciated.
>>>
>>> Thanks,
>>>
>>> PM
>>> 
>>

Re: [Jmol-users] Jmol 14.13.1

[Dean Johnston]

Yes - I have an example at: http://crystals.otterbein.edu/packing/index.html

Pick structure from the left menu and then click the “Show Contents of One
Unit Cell”. Works beautifully!

The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell
'cpk'; spacefill 1%;

Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:


Can the "slab" command be used to produce presentations equivalent to the
image linked below?

https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Dean Johnston]

This is listed on the Wavefunction, Inc. web site (
https://www.wavefun.com/products/databases.html):

Spartan Molecular Database (SMD), a collection of over 150,000 calculated
structures and associated properties of molecules, each obtained from as
many as ten different theoretical models (Hartree-Fock models with 3-21G*,
6-31G* and 6-311+G** basis sets, B3LYP and MP2 models with the 6-31G* and
6-311+G** basis sets, the EDF1 model with the 6-31G* basis set, the G3(MP2)
model and the T1 model)2, as well as a collection of approximately 1,200
small molecules bound to proteins and nucleotides from the PDB. New to the
SMD is the Spartan Infrared Database (SIRD), a collection of approximately
40,000 organic molecules, the infrared spectra of which have been obtained
from the EDF2/6-31G* model2 and which may be searched by matching to an
input (experimental) spectrum.  Current Spartan licenses include access to
a subset of the SMD.  Customers that purchase maintenance are provided with
the full SMD database on DVD ROM.  Licensing and additional information.



Not sure that’s what you’re looking for.

Dean

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Otterbein University • 1 South Grove St. • Westerville, OH 43081

On August 24, 2016 at 10:40:03 AM, Jennifer L. Muzyka (
jennifer.muz...@centre.edu) wrote:

iSpartan has something like that built into their app rather than
calculating things on the fly.  I’m not aware of any other database that
has the information you’re looking for, Bob.
Jennifer



Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Aug 24, 2016, at 10:34 AM, Robert Hanson  wrote:

I mean a database of common organic compounds, with molecular orbitals.
Spartan files or Gaussian output -- that sort of thing.
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Re: [Jmol-users] Hirshfeld Surfaces

[Dean Johnston]

I know that CrystalExplorer (http://hirshfeldsurface.net/) will generate
Hirshfeld surfaces, but I haven’t used it much. It relies on some kind of
wavefunction calculation (Tonto or Gaussian in the case of
CrystalExplorer), so I imagine that Jmol will similarly require more than
just coordinates.

Dean

On August 10, 2016 at 7:13:50 PM, Robert Hanson (hans...@stolaf.edu) wrote:

OK, well, do let me know if you find something. What I read is that it is
"relatively simple to implement".

Bob

On Tue, Aug 9, 2016 at 12:36 PM, S Westrip  wrote:

> Thanks
>
> No - I don't have an algorithm - literally just started to look into
> this...
>
> I was just using Jmol as my first "port of call" - Jmol often has the
> answers and saves we the work  :-)
>
> Cheers
>
> Simon
>
> On Aug 09, 2016, at 05:49 pm, Robert Hanson  wrote:
>
> No, it cannot. Have an algorithm?
>
> On Tue, Aug 9, 2016 at 11:40 AM, S Westrip 
> wrote:
>
>> Hello
>>
>> Does anyone know if Jmol can render Hirshfeld surfaces?
>>
>> Cheer
>>
>> Simon
>>
>> 
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Re: [Jmol-users] python scripting of Jmol

[Dean Johnston]

I’ve just started playing around with the CSD Python API 
(https://downloads.ccdc.cam.ac.uk/documentation/API/) - seems like Jmol would 
be ideal for displaying results from Python-generated searches.

Dean

On July 31, 2015 at 2:21:55 PM, Robert Hanson (hans...@stolaf.edu) wrote:

Q: Has anyone any experience with Python? I was just thinking that since Jmol 
can interact via a web socket, receiving script commands and replying with 
JSON, it should be very easy to script Jmol from Python.

It would just be a matter of starting Jmol as a socket listener, then working 
with that socket from Python.

Someone should try that; we could develop it more if necessary.

Any interest?

Bob


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Re: [Jmol-users] Jmol app vanishes in Yosemite

[Dean Johnston]

Eric,

I am not able to completely reproduce this (Mac OS 10.10.2, Macbook Pro 15”, 
Mid-2014), but I did notice that on the one display I could not position the 
Jmol app higher than a certain point. If I tried to move the app to the top of 
the screen, it would just move it about half-way down. I’m wondering if your 
computer is doing the same thing, but moving it completely off the screen.

I was able to modify this behavior by changing the “arrangement” of the screens 
using the Displays Preferences under System Preferences. Maybe the app is 
positioning itself based on information about the main screen, even though it 
has been moved to a secondary display.

Dean
On February 1, 2015 at 7:49:42 PM, Eric Martz (ema...@microbio.umass.edu) wrote:

This reports what I think is a bug in Mac Yosemite vis a vis the Jmol 
application (and perhaps any Java application).

A few days ago I upgraded from Mac OS 10.10.1 to 10.10.2 (current version of 
Yosemite). The Jmol application has a new behavior. When I drag its main window 
from my laptop screen into an external flatscreen (both desktops active), it 
vanishes. Mission control (showing all open apps and desktops) shows the Jmol 
windows but I can't get them into a working desktop, so I can't use Jmol. If 
you close Jmol and re-open it, it auto-vanishes.

No other application I have used has this behavior, but Jmol is the only java 
app I'm using.

The only way I've found to use the Jmol app:
1. Unplug my external flatscreen, and Jmol returns to my laptop screen.
2. I can plug my external flatscreen in again as long as I don't drag Jmol into 
it. I must use the Jmol app only in my laptop screen.

(New 15 MacBook Pro, shipped end of December 2014.)

Comments? Confirmation? Insights?

Eric
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[Jmol-users] unitcell and/or draw unitcell command changed between 13.3.3 and 14.1.6?

[Dean Johnston]

Jmol users list,

I’ve noticed a change in behavior of the unitcell/draw unitcell command 
somewhere between 13.3.3 and 14.1.6. I’m using it to draw representations of 
multiple unit cells of simple crystal structures like bcc, fcc, etc. I use the 
unitcell and draw unitcell commands to draw multiple representations of unit 
cells for an expanded lattice. In the later version (including 14.1.8), the 
unit cells end up spaced out” instead of contiguous. Picture and links below.

Dean Johnston

Jmol 13.3.3 (http://crystals.otterbein.edu/packing/packing-jmol13-3-3.html)
 — click on “simple cubic” on the left, then “Show 27 Unit Cells” on the right.

Jmol 14.1.6 (http://crystals.otterbein.edu/packing/packing-jmol14-1-6.html)
 — click on “simple cubic” on the left, then “Show 27 Unit Cells” on the right.





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Re: [Jmol-users] unitcell and/or draw unitcell command changed between 13.3.3 and 14.1.6?

[Dean Johnston]

hmm. What's this about, by the way? I hope we don't need that sort of thing. If 
we do, I need to fix something.
      var $j = jQuery.noConflict();

I used the Prototype.js library for these pages. It uses $() syntax for DOM 
queries like jQuery. I’m slowly removing the dependence on Prototype.js, but 
these pages haven’t been updated in a while.

On February 5, 2014 at 7:52:19 PM, Robert Hanson (hans...@stolaf.edu) wrote:
Looks like a bug in DRAW. I will fix it.

hmm. What's this about, by the way? I hope we don't need that sort of thing. If 
we do, I need to fix something.

   var $j = jQuery.noConflict();





On Wed, Feb 5, 2014 at 5:33 PM, Dean Johnston djohnsto...@gmail.com wrote:
Jmol users list,

I’ve noticed a change in behavior of the unitcell/draw unitcell command 
somewhere between 13.3.3 and 14.1.6. I’m using it to draw representations of 
multiple unit cells of simple crystal structures like bcc, fcc, etc. I use the 
unitcell and draw unitcell commands to draw multiple representations of unit 
cells for an expanded lattice. In the later version (including 14.1.8), the 
unit cells end up spaced out” instead of contiguous. Picture and links below.

Dean Johnston

Jmol 13.3.3 (http://crystals.otterbein.edu/packing/packing-jmol13-3-3.html)
 — click on “simple cubic” on the left, then “Show 27 Unit Cells” on the right.

Jmol 14.1.6 (http://crystals.otterbein.edu/packing/packing-jmol14-1-6.html)
 — click on “simple cubic” on the left, then “Show 27 Unit Cells” on the right.




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Re: [Jmol-users] Should translucency be additive?

[Dean Johnston]

Thanks Bob - the simple solution is just to make the main object opaque (it
was already nearly opaque).  Then all the translucencies look just fine.  I
don't really know why I made it translucent to begin with.

Dean


On Mon, Aug 8, 2011 at 1:35 PM, Robert Hanson hans...@stolaf.edu wrote:

 Jmol should show proper additive color for an opaque layer plus two
 translucent layers in front of it. After that, we cheat and ignore anything
 behind the front two translucent layers. That can cause some strangeness if
 you look very closely, as I suspect you are, Dean, but hopefully you can
 live with that. A truly proper treatment requires ordering of all pixels in
 space. No real-time system is able to handle that that I know of. (The
 standard OpenGL format cheats in other ways.) But I think perhaps PovRAY
 would do that right. So if you need exquisite translucency, export to
 PovRAY.

 Bob


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[Jmol-users] Should translucency be additive?

[Dean Johnston]

Jmol'ers,

  I just noticed an interesting effect in Jmol.  I have a model with several
planes having different levels of translucency.  But Jmol only seems to use
the translucency of the frontmost plane when looking at something that falls
behind two translucent planes.  I suspect this is in the name of efficiency,
but didn't know if anyone else had noticed this.

Dean
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Re: [Jmol-users] Molecular view (CIF)

[Dean Johnston]

Bob,

I had a question about that  - does having a large number (i.e. thousands)
of hidden atoms slow Jmol down at all relative to deleting unwanted atoms?
In my case I knew that I wouldn't need to display some atoms, so I didn't
care if they were deleted.  But I didn't know if there was a benefit to
deleting them.  I agree that hiding them could let you switch between the
different packing choices without having to re-load the cif.

Dean

On Mon, Jul 18, 2011 at 10:38 AM, Robert Hanson hans...@stolaf.edu wrote:

 Thanks, Dean.

 Minor point: Generally I would recommend display... instead of delete
 not...  That gives you more flexibility.

 Bob

 On Sun, Jul 17, 2011 at 9:29 PM, Dean Johnston djohnsto...@gmail.comwrote:

 Simon,

 Here's what I've used.  It obviously only works for molecular systems and
 can be somewhat slow for very large molecules/unit cells.  Bob can probably
 figure out a more efficient way to do this, but it works for me.  In these
 examples I've deleted any molecules that I don't want to see - you may want
 to just hide/display molecules instead.

 (1) I think this is equivalent to what Bob had suggested before - similar
 to Mercury's include atoms in molecules where *Any* atom fits.

 load xxx.cif {333 777 1}; delete not within(molecule, unitcell);


 (2) Or (more complicated) - I think this is similar to Mercury's include
 atoms in molecules whose *Centroids* fit.

 load xxx.cif {333 777 1};
  delete not within(molecule, unitcell);
 n = getProperty(moleculeInfo).size;
 for (var i=1; i=n; i++)
 {
 select molecule=i;
 if (({selected}.fx  -0.001) || ({selected}.fx  1.001) ||
 ({selected}.fy  -0.001) || ({selected}.fy  1.001) || ({selected}.fz 
 -0.001) || ({selected}.fz  1.001))
 { hide (hidden || {selected}); }
 };
 delete hidden;

 Dean


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Re: [Jmol-users] Molecular view (CIF)

[Dean Johnston]

Simon,

Here's what I've used.  It obviously only works for molecular systems and
can be somewhat slow for very large molecules/unit cells.  Bob can probably
figure out a more efficient way to do this, but it works for me.  In these
examples I've deleted any molecules that I don't want to see - you may want
to just hide/display molecules instead.

(1) I think this is equivalent to what Bob had suggested before - similar to
Mercury's include atoms in molecules where *Any* atom fits.

load xxx.cif {333 777 1}; delete not within(molecule, unitcell);


(2) Or (more complicated) - I think this is similar to Mercury's include
atoms in molecules whose *Centroids* fit.

load xxx.cif {333 777 1};
delete not within(molecule, unitcell);
n = getProperty(moleculeInfo).size;
for (var i=1; i=n; i++)
{
select molecule=i;
if (({selected}.fx  -0.001) || ({selected}.fx  1.001) ||
({selected}.fy  -0.001) || ({selected}.fy  1.001) || ({selected}.fz 
-0.001) || ({selected}.fz  1.001))
{ hide (hidden || {selected}); }
};
delete hidden;

Dean
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Re: [Jmol-users] copy text from Jmol console

[Dean Johnston]

Just like Bob said, on my Mac (10.6.7, Java 1.6.0_24) it depends on whether
it is the signed applet (or stand alone app).  With the signed applet or
application, I find it handy to select text from the Jmol console (or the
script editor) and then click and drag it onto the desktop to create a text
clipping.  I can then drag those into other text editors or back into the
Jmol console fairly easily.  Alas, this does not work with the unsigned
applet for me.  I haven't tried using the Java console.

Dean

On Fri, May 6, 2011 at 2:45 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr
 wrote:

 Copying from the java console on a Mac (10.6 Safari) works fine for me. I
 can't remember if I made a specific setup, but the java console opens
 automatically when I load a webpage with an applet. Otherwise, you can
 probably call it via the top menu bar coffee icon.
 -Paul

 Le 6 mai 2011 à 20:05, Robert Hanson a écrit :

  again, the workaround is simply to copy from the Java console, not the
 Jmol console. I know, with Macs that might be hard to find. Someone with a
 Mac can fill us in on that. It looks like the Jmol console can only be
 clipped from using the signed applet. I believe this is the intended
 behavior of Java, not a bug in Java, but I could be wrong.
 
  Bob
 




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[Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell

[Dean Johnston]

Does anybody know if there is a relatively simple way to find all the
crystallographic symmetry elements within a unit cell using Jmol?  For
example, if there is an inversion center at the origin, there may be several
other inversion centers generated by the space group symmetry.  I can see
some of them by asking Jmol for the symmetry relationship(s) between two
atoms or two molecules.  But I'm interested in generating a list of all the
inversion centers (or glide planes, etc.) within the cell.  Thanks for any
insights.

Dean
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Re: [Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell

[Dean Johnston]

OK - something along those lines was what I was thinking - thanks for the
code example.

Dean

On Thu, Apr 21, 2011 at 12:15 PM, Robert Hanson hans...@stolaf.edu wrote:

 Dean,

 Well, it's just the product of all the symmetry operators. Get the
 collection of symmetry operators and multiply them until you get a complete
 set. I'll have to think about whether you can get all those as variables
 Yes, I think you can. You would have to normalize them to stay within the
 unit cell.

 strsymops = getproperty(auxiliaryinfo.models[1].symmetryOperations)
 print strsymops.length
 op = []

 for (var i = 1; i  strsymops.length; i++) {
op[i] = symop(i)
print  + strsymops[i] + \n + op[i]
 }

 op is then an array of the matrices, and you can multiply these at will.

 The problem you might have is whether there is a simple way to limit this
 to within the unit cell. For that, it's probably just as well to take a
 random point and keep operating on it, returning its unit cell coordinates
 each time. Anyway, since you can get the matrices for the space group
 operations, you should be able to get all combinations of them.

 Bob

 On Thu, Apr 21, 2011 at 10:45 AM, Dean Johnston djohnsto...@gmail.comwrote:

 Does anybody know if there is a relatively simple way to find all the
 crystallographic symmetry elements within a unit cell using Jmol?  For
 example, if there is an inversion center at the origin, there may be several
 other inversion centers generated by the space group symmetry.  I can see
 some of them by asking Jmol for the symmetry relationship(s) between two
 atoms or two molecules.  But I'm interested in generating a list of all the
 inversion centers (or glide planes, etc.) within the cell.  Thanks for any
 insights.

 Dean


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Re: [Jmol-users] Jmol and crystallography: the paper

[Dean Johnston]

Excellent - lots of beautiful examples showing why Jmol is a killer app!

Dean

On Thu, Sep 2, 2010 at 3:21 PM, Robert Hanson hans...@stolaf.edu wrote:

 *This just in!
 *

 *J. Appl. Cryst.* (2010). *43*  [ 
 doi:10.1107/S0021889810030256http://dx.doi.org/10.1107/S0021889810030256]
 *Jmol* - a paradigm shift in crystallographic visualization R. M. 
 Hansonhttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Hanson%2C%20R%2EM%2E

 *Synopsis: *Features of *Jmol* that allow new ways for students to
 interact with three-dimensional virtual models and explore molecular and
 crystallographic symmetry are described.

 Online 1 September 2010

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 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


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Re: [Jmol-users] Appending with inline data not working in 12.0

[Dean Johnston]

Thanks for the clarification on append versus set appendNew - I was just
looking for a reason that the data wasn't being appended.  Seems to work
now.

Dean

On Sun, Jul 25, 2010 at 1:05 AM, Robert Hanson hans...@stolaf.edu wrote:

 By the way, DATA is now merged with LOAD. You basically just use the load
 command with all its options (append, filter, {n n n}, unitcell, spacegroup,
 etc.) with the data command included in it:

 load data append inline
 ..
 end data append inline packed {3 3 3}


 Bob


 On Sat, Jul 24, 2010 at 9:54 PM, Dean Johnston djohnsto...@gmail.comwrote:

 Bob,

   Just testing 12.0.RC28_dev and for my site the DATA command with the
 append option (set appendNew true) appears not to work properly (models are
 just replaced).  Sorry I don't have time to do any more detailed testing.  I
 didn't have to set the appendNew flag in the past - I think in 11.8 I just
 had append in the first line of the inline data.

 Dean


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[Jmol-users] Appending with inline data not working in 12.0

[Dean Johnston]

Bob,

  Just testing 12.0.RC28_dev and for my site the DATA command with the
append option (set appendNew true) appears not to work properly (models are
just replaced).  Sorry I don't have time to do any more detailed testing.  I
didn't have to set the appendNew flag in the past - I think in 11.8 I just
had append in the first line of the inline data.

Dean
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[Jmol-users] Crash with rotate symop # (cif file)

[Dean Johnston]

I'm having fun playing with all the wonderful crystallography stuff built
into Jmol, but I'm getting the following when I try the ROTATE with the
SYMOP option.  It seems to happen with both the applet and the application -
with a variety of CIF files.

Exception in thread QueueThread0 java.lang.NullPointerException
at org.jmol.util.Quaternion.set(Quaternion.java:130)
at org.jmol.util.Quaternion.init(Quaternion.java:68)
at org.jmol.script.ScriptEvaluator.rotate(ScriptEvaluator.java:8581)
at
org.jmol.script.ScriptEvaluator.instructionDispatchLoop(ScriptEvaluator.java:5014)
at
org.jmol.script.ScriptEvaluator.evaluateCompiledScript(ScriptEvaluator.java:229)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:4113)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
at java.lang.Thread.run(Thread.java:613)


Dean
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Re: [Jmol-users] draw ARC won't stay FIXED during animation

[Dean Johnston]

Yep - problem fixed.  Thanks, Bob!

On Tue, Mar 9, 2010 at 9:18 AM, Robert Hanson hans...@stolaf.edu wrote:

 I think I have this fixed.

 On Mon, Mar 8, 2010 at 8:35 AM, Dean Johnston djohnsto...@gmail.comwrote:

 I'll post one as soon as I can - my current observations are on a complex
 page - I'll try and nail it down to the simplest possible case.

 Dean


 On Mon, Mar 8, 2010 at 8:59 AM, Robert Hanson hans...@stolaf.edu wrote:

 example please. I was working there recently.

 On Sat, Mar 6, 2010 at 9:27 PM, Dean Johnston djohnsto...@gmail.comwrote:

 Possible bug with newer version of Jmol (11.9.32).

 I'm finding that the arcs that I'm drawing (with the FIXED option) are
 popping on and off during animations.  This glitch does not appear in Jmol
 11.6.  Unless the syntax has changed, I think this might be a bug.  All
 other objects created using the DRAW command (lines, planes, cylinders) are
 just fine -- only the arcs are affected.

 Dean


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Re: [Jmol-users] draw ARC won't stay FIXED during animation

[Dean Johnston]

I'll post one as soon as I can - my current observations are on a complex
page - I'll try and nail it down to the simplest possible case.

Dean

On Mon, Mar 8, 2010 at 8:59 AM, Robert Hanson hans...@stolaf.edu wrote:

 example please. I was working there recently.

 On Sat, Mar 6, 2010 at 9:27 PM, Dean Johnston djohnsto...@gmail.comwrote:

 Possible bug with newer version of Jmol (11.9.32).

 I'm finding that the arcs that I'm drawing (with the FIXED option) are
 popping on and off during animations.  This glitch does not appear in Jmol
 11.6.  Unless the syntax has changed, I think this might be a bug.  All
 other objects created using the DRAW command (lines, planes, cylinders) are
 just fine -- only the arcs are affected.

 Dean


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[Jmol-users] draw ARC won't stay FIXED during animation

[Dean Johnston]

Possible bug with newer version of Jmol (11.9.32).

I'm finding that the arcs that I'm drawing (with the FIXED option) are
popping on and off during animations.  This glitch does not appear in Jmol
11.6.  Unless the syntax has changed, I think this might be a bug.  All
other objects created using the DRAW command (lines, planes, cylinders) are
just fine -- only the arcs are affected.

Dean
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Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)

[Dean Johnston]

Oh - this is great!  Exactly what I wanted - in a straightforward
implementation - nicely done. Thanks Bob!

Dean

On Tue, Mar 2, 2010 at 8:20 AM, Robert Hanson hans...@stolaf.edu wrote:

 Dean, I just checked in code that does this better.

 Bob


 On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson hans...@stolaf.edu wrote:

 Well, that wasn't so bad.

 isosurface na1 cap unitcell center {atomno=1} sphere 2.0

 does what you see there for one of the atoms

 isosurface na1 slab unitcell center {atomno=1} sphere 2.0

 does that, but doesn't close the ends. Kind of cool that this addition
 only about 20 lines of code. Fun!

 So the solution is to create a sphere isosurface for each.

 Kind of neat that the unitcell doesn't have to be orthogonal.

 Also works with boundbox.

 Bob

 On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston djohnsto...@gmail.comwrote:

 Jmol Users,

   Here's something I've always wanted to do with Jmol -- use clipping
 planes to show students the *fractions* of atoms in a unit cell (similar
 to attached image of NaCl generated using POV-Ray).  I know I can use slab
 HKL and depth HKL, but those don't slice through the atoms like the normal
 slab and depth commands.  I think there was a thread a while back on
 something like this, but I couldn't track it down.  I've also thought about
 generating isosurfaces to represent the fractions of atoms, but that seemed
 tedious.

 Dean


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 phone: 507-786-3107


 If nature does not answer first what we want,
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 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




 --
 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.

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Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)

[Dean Johnston]

Yes - you're ahead of me again.  I like having the isosurfaces tied to atoms
- certainly easier than creating one for each atom.  I can't wait to set up
some web pages using this...

Dean

On Wed, Mar 3, 2010 at 8:45 AM, Robert Hanson hans...@stolaf.edu wrote:

 Better than that.

 Dean, once again you have such a great idea, and I am delighted to say it
 was relatively easy to implement. Here's what I just checked in:

 LcaoCartoon now has a CPK option. This option creates a sphere at the
 radius of the currently set spacefill. (The s option creates a sphere of a
 standard radius.) That may seem a bit odd, but the idea is that you can set
 the radius using spacefill and then apply that radius to LCAOCARTOON for
 this special purpose.

 Why LcaoCartoon? Because LcaoCartoon is a form of isosurface, and it allows
 tying an isosurface to a specific atom.
 And since isosurfaces now can be slabbed and capped by planes,
 boundingboxes, and unitcells, so can LcaoCartoons.

 So here's how you would do that:

 select {theAtoms}
 spaceFill 2.0 # perhaps
 color translucent blue # color also used in lcaocartoon CPK method
 lcaocartoon CAP unitcell cpk
 spaceFill off

 If this seems too weird, we can talk about another way of doing it, but for
 now this should work.

 Bob




 On Wed, Mar 3, 2010 at 7:44 AM, Dean Johnston djohnsto...@gmail.comwrote:

 Oh - this is great!  Exactly what I wanted - in a straightforward
 implementation - nicely done. Thanks Bob!

 Dean


 On Tue, Mar 2, 2010 at 8:20 AM, Robert Hanson hans...@stolaf.edu wrote:

 Dean, I just checked in code that does this better.

 Bob


 On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson hans...@stolaf.eduwrote:

 Well, that wasn't so bad.

 isosurface na1 cap unitcell center {atomno=1} sphere 2.0

 does what you see there for one of the atoms

 isosurface na1 slab unitcell center {atomno=1} sphere 2.0

 does that, but doesn't close the ends. Kind of cool that this addition
 only about 20 lines of code. Fun!

 So the solution is to create a sphere isosurface for each.

 Kind of neat that the unitcell doesn't have to be orthogonal.

 Also works with boundbox.

 Bob

 On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston 
 djohnsto...@gmail.comwrote:

 Jmol Users,

   Here's something I've always wanted to do with Jmol -- use clipping
 planes to show students the *fractions* of atoms in a unit cell
 (similar to attached image of NaCl generated using POV-Ray).  I know I can
 use slab HKL and depth HKL, but those don't slice through the atoms like
 the normal slab and depth commands.  I think there was a thread a while 
 back
 on something like this, but I couldn't track it down.  I've also thought
 about generating isosurfaces to represent the fractions of atoms, but that
 seemed tedious.

 Dean


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[Jmol-users] Multiple clipping planes (using slab/depth HKL)

[Dean Johnston]

Jmol Users,

  Here's something I've always wanted to do with Jmol -- use clipping planes
to show students the *fractions* of atoms in a unit cell (similar to
attached image of NaCl generated using POV-Ray).  I know I can use slab HKL
and depth HKL, but those don't slice through the atoms like the normal
slab and depth commands.  I think there was a thread a while back on
something like this, but I couldn't track it down.  I've also thought about
generating isosurfaces to represent the fractions of atoms, but that seemed
tedious.

Dean
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Re: [Jmol-users] Are others experiencing very broken javascript and Jmol pages in IE8?

[Dean Johnston]

I haven't noticed any severe problems with the testing I've done (WinXP SP3,
IE7 and IE8).  But I spend most of my time with Firefox.

Dean

On Sun, Oct 4, 2009 at 7:54 PM, Robert Hanson hans...@stolaf.edu wrote:

 In case it's any consolation -- Windows 7 running MSIE 8.0.7100.0 works
 just fine. It's possible that one of my family members enabled scripting for
 applets, but I doubt it. It's a recent build. Do we need to trap this in
 jmolScript()?



 On Sun, Oct 4, 2009 at 11:13 AM, Jonathan Gutow gu...@uwosh.edu wrote:

 Angel,
Thanks for the offer.  I've found the problem for web pages off of
 servers.  It appears that (as is often the case in MS products) you
 have to turn things on (and off) in more than one place to get them to
 work.  In IE 8 just choosing to allow active content when warned (ie
 Javascript and ActiveX) does not work.  You also have to go to Tools 
 Internet Options  Security Tab  Custom Level... button and then make
 sure that Active Scripting and Scripting of Applets is enabled.  I
 would guess many people will not be able to get pages with applets and
 javascript working in IE8.

I haven't found how to get it to behave for local files.

Two comments:
 1) IE8 appears to be 4 - 10 times slower than Firefox.
 2) IE8 appears to have a nice developer's tools for debugging.
 However, on my test machine it is so slow, that I don't think I will
 have the patience to use it.

 Jonathan
 On Oct 4, 2009, at 7:27 AM, jmol-users-requ...@lists.sourceforge.net
 wrote:

  From: Angel Herr?ez angel.herr...@uah.es
  Subject: Re: [Jmol-users] Are others experiencing very broken
javascript and  Jmol pages in IE8?
  To: jmol-users@lists.sourceforge.net
  Message-ID: 4ac873c3.29219.d863...@angel.herraez.uah.es
  Content-Type: text/plain; charset=US-ASCII
 
  Dear Jonathan
 
  I haven't seen any major problems like you describe -- but I don't
  test IE often.
  I've had XPsp3 for a long time now,so I would not suspect that.
  IE8 is another business, it seems to handle things a bit different,
  has a better support for
  DOM/CSS standards, and particularly it has a new, better (well, at
  least it's something) error
  report for javascript, so things that didn't show up in IE7 may now
  be made prominent.
 
  If you can point out to some of your problem pages, I may test them
  in my system.

  Dr. Jonathan H. Gutow
 Chemistry Department gu...@uwosh.edu
 UW-Oshkosh   Office:920-424-1326
 800 Algoma Boulevard FAX:920-424-2042
 Oshkosh, WI 54901
  http://www.uwosh.edu/facstaff/gutow







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Re: [Jmol-users] Jmol applet blinking during scripted animations with Safari

[Dean Johnston]

Just to follow up.  You were correct, Bob - the blinking had nothing to do
with Jmol.  It was actually the CSS tabs on the top of the page (along
with the slider control).  A slight change in the CSS code that creates the
tabs (removing the float property) appears to have fixed the problem.

Dean

On Wed, Apr 1, 2009 at 11:34 PM, Robert Hanson hans...@stolaf.edu wrote:

 Dean, it appears to me to be the slider control. Moving it triggers a
 repaint of the applet, which not happening smoothly. It's possible that Jmol
 is at fault. But I'm not sure. Try creating the applet with a different
 background color. If you can avoid the white/black switch, perhaps it won't
 be so noticeable.

 On Wed, Apr 1, 2009 at 9:44 PM, Dean Johnston djohnsto...@gmail.comwrote:

 Jmol users,

 Has anybody else noticed the Jmol applet blinking (flashing black) when
 being scripted via Javascript in Safari?  I've had some users complain with
 my website (http://symmetry.otterbein.edu/gallery), but I'm not sure if
 it's something specific I'm doing.  It can be rather distracting since all
 my animations are run via Javascipt.

 I see the behavior in Safari 3 and Safari 4 (beta) on OS X.  I don't see
 it with Firefox or with any Windows browser.  I'm using OS X 10.5.6.  The
 web site uses Jmol 11.6.  I've tested with the latest Jmol release and see
 the same behavior.

 Thanks for any help or suggestions.

 Dean


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 phone: 507-786-3107


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Re: [Jmol-users] problem to take into account changes to a file.xyz in the Jmol applet

[Dean Johnston]

I don't know if this will work for your situation, but I use a Firefox
extension called Web Developer (
https://addons.mozilla.org/en-US/firefox/addon/60).  It adds a toolbar that
allows you to temporarily disable the cache (along with many other useful
features).

Dean

2009/4/2 Angel Herraez angel.herr...@uah.es

 Hello Benjamin

 Your problem is probaly related to the Java cache in the browser.
 This a browser-specific problem, per user.
 You can fix it by manually clearing the Java cache before each
 reload. There are instructions in the Jmol Wiki, Running Jmol,
 Troubleshooting:
 http://wiki.jmol.org:81/index.php/Troubleshooting/Java_Problems#Java_c
 ache

 I don't think there is any other solution, or an automatic one. Maybe
 you can disable the Java cache.

 The only other fix is to use a different filename each time.




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[Jmol-users] Jmol applet blinking during scripted animations with Safari

[Dean Johnston]

Jmol users,

Has anybody else noticed the Jmol applet blinking (flashing black) when
being scripted via Javascript in Safari?  I've had some users complain with
my website (http://symmetry.otterbein.edu/gallery), but I'm not sure if it's
something specific I'm doing.  It can be rather distracting since all my
animations are run via Javascipt.

I see the behavior in Safari 3 and Safari 4 (beta) on OS X.  I don't see it
with Firefox or with any Windows browser.  I'm using OS X 10.5.6.  The web
site uses Jmol 11.6.  I've tested with the latest Jmol release and see the
same behavior.

Thanks for any help or suggestions.

Dean
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Re: [Jmol-users] AJAX applications and Jmol and Jmol.js

[Dean Johnston]

I've used the Prototype.js library pretty extensively in my pages (
http://symmetry.otterbein.edu).  I store my structures as JSON files which I
can read and evaluate using the AJAX functionality in the prototype
library.  I also do some select DOM replacement to generate tables of
checkboxes and other controls.  I haven't had any difficulty getting the
Jmol.js functions to work with what I've written.

Dean

On Wed, Dec 17, 2008 at 1:24 PM, Paul Pillot 
paul.pil...@ac-orleans-tours.fr wrote:

 I did that a couple years ago on a project involving prototype mixed
 with jmol.js without any trouble.
 http://librairiedemolecules.education.fr/outils/xtal0/xtal.htm#
 It's beta and not working anymore as it should, due to changes in the
 back-end database. You can still click on the Fichier link and make
 a search. A message alerting that no file has been found should be
 displayed.
 I don't know if that would help as this page uses versions of theses
 libraries dating from 2 years ago...
 Paul


 Le 17 déc. 08 à 10:50, Raphael André Bauer a écrit :

  Hey list,
 
 
  I am curious if anybody managed to get Jmol up and running in a AJAX
  application that replaces the DOM. In another thread I discussed an
  issue where I had severe problems using the GWT (well, the GWT is
  somehow special as well). My experience is, that the applet (using the
  object tag) works fine, but the Jmol.js (providing very useful
  functionality) breaks something (Hard to debug in the GWT for me). I
  know that Jmol.js does not play together well with the prototype AJAX
  library as well.
 
  So - is anybody using Jmol in such a AJAX scenario? If yes - with what
  AJAX library?
 
 
  Thanks!
 
  Raphael
 
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Re: [Jmol-users] Using the sync command for 3D/stereographic visualization (on a GeoWall)

[Dean Johnston]

You're too fast!  I just got my single applet version working (I think - we
don't have a GeoWall setup here).  Centering/aligning shouldn't be a problem
if I can properly detect the window width and position using CSS.  Thanks!

Dean

On Tue, Nov 25, 2008 at 3:16 PM, Robert Hanson [EMAIL PROTECTED] wrote:

 Dean, try http://chemapps.stolaf.edu/jmol/docs/examples-11/syncstereo.htm

 I know for your use you need the table cells centered -- some
 experimentation there will be necessary.

 The new command is:

  sync * stereo


 files are in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip

 Bob


 On Mon, Nov 24, 2008 at 8:24 AM, Robert Hanson [EMAIL PROTECTED] wrote:
  OK, do let me know how that goes. I have a setup here I'm supposed to
  try Jmol on as well.
 
  In the mean time, I'll think about the possibility of using one applet
  to transmit screen buffers to two different applet windows. Sort of a
  dummy applet idea. You would do all control on one, but the matching
  stereo image would be sent to the other.
 
  Bob
 
 
  On Mon, Nov 24, 2008 at 8:01 AM, Dean Johnston [EMAIL PROTECTED]
 wrote:
  Thanks for the clarification.  I think I'll go for the slight redesign
 and
  use the stereo command.  I don't want to give even more people headaches
  that might result from a slight delay between the two :-|
 
  Dean
 
 
  On Mon, Nov 24, 2008 at 7:45 AM, Robert Hanson [EMAIL PROTECTED]
 wrote:
 
  Dean, just to be clear -- I was missing something as well -- If you
  are using mouse syncing and not script syncing, then you should be
  able to send any rotation commands you want to one of the applets and
  the other won't respond. No need to turn sync on and off. So you
  should be able to rotate the models independently with scripting to
  set up the stereo anytime, even with syncing on. Since you are syncing
  with the mouse, you don't have to worry about any rotations you would
  do with scripting -- they won't be transmitted anyway. You just have
  to worry about resets, file loads, and such, where in each case you
  will have to make sure both applets load (using script syncing?) and
  then rotate one model and not the other. (Yes, you could also do both
  -- one one way and the other the other way, but Jmol just rotates the
  right-hand one.) The proper angle is 3 degrees (-1.5 and 1.5) for
  overlaid stereo. 5 degrees is for side-by-side stereo.
 
  That said, I still think you are asking too much of sync. Stereo
  should be absolutely simultaneous projection. There WILL be some
  delay, especially for larger structures.
 
  Are you sure you can't have buttons and such below the applet and
  still have a good stereo effect with the Jmol stereo command?
 
  Bob
 
 
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 http://www.stolaf.edu/people/hansonr
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Re: [Jmol-users] Using the sync command for 3D/stereographic visualization (on a GeoWall)

[Dean Johnston]

I'm not sure it's that easy - I agree that rotating one model as you
describe would give you stereo perspective initially. But as soon as you
rotate the model(s) you destroy the difference in perspective.  For example,
if I have two parallel lines pointing directly at the viewer, to give
perspective I could rotate the left one -2.5 degrees around y and the
right one +2.5 degrees around y.  If I then rotate 90 degrees around x, I'll
see two lines that are not parallel, even though that's what I should see.

What I need is for the two applets to show two different perspectives on the
same model such that the perspective differences are maintained even while
rotating.  Am I missing something easy here?

Dean


On Sun, Nov 23, 2008 at 7:51 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 Oh, I see. That's easy!

 Just turn sync off, rotate one model -5 degrees around the Y axis
 (rotate y -5), and then turn mouse syncing back on.
 They will now track properly as stereo images.


 On Sat, Nov 22, 2008 at 9:22 PM, Dean Johnston [EMAIL PROTECTED]
 wrote:
  Bob,
 
  I guess I was asking if the sync command could be modified (feature
  request!) such that two different perspectives could be shown in two
  different applets.  (I realize that the delay might be an issue, but in
 my
  testing on my computer it wasn't noticeable - FYI, I only have syncMouse
 on.
  If syncScript is on then the delay is significant.)
 
  As far as George's solution - if I make the applet the full width of both
  screens then it doesn't leave room for my other controls like molecule
  selection, etc.  I could rewrite my pages to put the controls above or
 below
  the applet, but I was hoping that sync might work.  Thanks.
 
  Dean
 
 
  On Sat, Nov 22, 2008 at 4:37 PM, Robert Hanson [EMAIL PROTECTED]
 wrote:
 
  Dean, you need to use stereo, not sync. Sync will certainly drive the
  viewer nuts -- there will be a slight delay between eyes. George
  Lisensky has used Jmol with GeoWall -- ask him how he does it. I'm
  pretty sure you just make the applet or application 2048 pixels wide
  and then direct the left side of the screen to one projector and the
  right side to the other.
 
  Bob
 
 

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Re: [Jmol-users] Using the sync command for 3D/stereographic visualization (on a GeoWall)

[Dean Johnston]

Bob,

I guess I was asking if the sync command could be modified (feature
request!) such that two different perspectives could be shown in two
different applets.  (I realize that the delay might be an issue, but in my
testing on my computer it wasn't noticeable - FYI, I only have syncMouse on.
If syncScript is on then the delay is significant.)

As far as George's solution - if I make the applet the full width of both
screens then it doesn't leave room for my other controls like molecule
selection, etc.  I could rewrite my pages to put the controls above or below
the applet, but I was hoping that sync might work.  Thanks.

Dean


On Sat, Nov 22, 2008 at 4:37 PM, Robert Hanson [EMAIL PROTECTED] wrote:

 Dean, you need to use stereo, not sync. Sync will certainly drive the
 viewer nuts -- there will be a slight delay between eyes. George
 Lisensky has used Jmol with GeoWall -- ask him how he does it. I'm
 pretty sure you just make the applet or application 2048 pixels wide
 and then direct the left side of the screen to one projector and the
 right side to the other.

 Bob


 On Fri, Nov 21, 2008 at 9:15 PM, Dean Johnston [EMAIL PROTECTED]
 wrote:
  Jmol users,
 
I've had a request to make my Jmol pages work with a GeoWall-type
 setup.
  (If you're not familiar with GeoWall (www.geowall.org), it's a low-cost
  stereo projection system.  You setup a computer with a dual-head video
 card,
  two projectors with polarizing filters, and align the two projectors on
 the
  same screen.  You can then use a variety of software (including Jmol) to
  project two orientations, one to each projector -- if you're wearing
  properly polarized glasses you get a very nice 3D effect.)
 
I'd like to use the SYNC command to do the same thing the STEREO
 command
  does, but between two applets. But I don't know that this an option --
 it's
  probably a feature request.  The stereo command doesn't work for my web
  pages because the Jmol applet sits in the middle of the page and I need a
  second applet to appear in the same position on the other monitor
 (showing
  the other perspective).  Has anybody tried to do something like this?
  Thanks.
 
  Dean
 
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[Jmol-users] Using the sync command for 3D/stereographic visualization (on a GeoWall)

[Dean Johnston]

Jmol users,

  I've had a request to make my Jmol pages work with a GeoWall-type setup.
(If you're not familiar with GeoWall (www.geowall.org), it's a low-cost
stereo projection system.  You setup a computer with a dual-head video card,
two projectors with polarizing filters, and align the two projectors on the
same screen.  You can then use a variety of software (including Jmol) to
project two orientations, one to each projector -- if you're wearing
properly polarized glasses you get a very nice 3D effect.)

  I'd like to use the SYNC command to do the same thing the STEREO command
does, but between two applets. But I don't know that this an option -- it's
probably a feature request.  The stereo command doesn't work for my web
pages because the Jmol applet sits in the middle of the page and I need a
second applet to appear in the same position on the other monitor (showing
the other perspective).  Has anybody tried to do something like this?
Thanks.

Dean
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Re: [Jmol-users] Translucent cylinder disappears when viewed edge on

[Dean Johnston]

Just confirming that the fix works for me.  Thanks Bob.

Dean

On Sun, Oct 5, 2008 at 8:20 PM, Robert Hanson [EMAIL PROTECTED] wrote:

 this is fixed for Jmol 11.6

 On Sat, Oct 4, 2008 at 12:20 AM, Dean Johnston [EMAIL PROTECTED]wrote:

 Here's an odd one.  My (very short) translucent cylinders disappear when
 viewed within a few degrees of edge-on.  To be more exact, the center
 disappears while the edge remains visible.  These are the same type of
 cylinders that are generated by the draw pointgroup command.  I've only
 started to notice this with the most recent version (11.6.RC19).

 Here's the command.

 draw plane1_disk width 6.2001 cylinder {-0.0300 0. 0.} {0.0300
 0. 0.} color translucent orange fixed;

 Dean

 P.S.  If it's any help, the angle at which it disappears gets smaller if
 you turn on antialiasDisplay.



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


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

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

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Re: [Jmol-users] State script not scaling arcs properly

[Dean Johnston]

Yes - works perfectly.  Thanks Bob!

Dean

On Tue, Sep 30, 2008 at 10:27 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 Dean, please confirm that this is fixed.


 On Sat, Sep 27, 2008 at 11:32 AM, Robert Hanson [EMAIL PROTECTED]wrote:

 fixed for Jmol 11.6.RC17


 On Sat, Sep 27, 2008 at 10:46 AM, Robert Hanson [EMAIL PROTECTED]wrote:

 ok, that should be a simple fix. simple Jmol script?


 On Fri, Sep 26, 2008 at 1:17 AM, Dean Johnston [EMAIL PROTECTED]wrote:

 Bob,

   I'm finding that my state script doesn't properly reproduce the scale
 of the arcs.  They should be the same size as the disks (see the attached
 the Jmol state file).  If this has been fixed since RC_12 then ignore this.

 Dean


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


 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
 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




 --
 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

 -
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 challenge
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Re: [Jmol-users] jmol movie

[Dean Johnston]

I can view it (using QuickTime player) on a Mac (OS X 10.5.5).  It shows up
as a 500x500 movie - looks pretty good to me and plays very fast (it's done
within less than 5 seconds).

Dean

On Wed, Oct 1, 2008 at 10:25 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 Question: Can you watch this movie on your machine? If so, how's the
 resolution?

 http://www.stolaf.edu/people/hansonr/temp/rasraf.avi

 It's supposed to be 145 frames of a molecular dynamics calculation. It was
 created using the following Jmol script followed by running a program called
 VideoMach:

 function createFrame
  var fname = movie_+_frameID[-2][0] + .jpg
  write image 500 500 @fname
 end function

 function createMovie
  var nframes = {*}.model.max
  for (var i = 1; i = nframes; i = i + 1)
frame @i
createFrame
  end for
 end function

 createMovie


 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

 -
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 challenge
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Re: [Jmol-users] Jmol-users Digest, Vol 29, Issue 5

[Dean Johnston]

Yes, exactly - Bob fixed it for RC19.  Thanks

Dean

On Fri, Oct 3, 2008 at 4:42 AM, Nick Greeves [EMAIL PROTECTED]wrote:

 Hi Dean,Something like this? http://www.chemtube3d.com/BenzeneMOs.html
 I use connect 2 (carbon) (carbon) AROMATIC;

 All the best

 Nick

 --

 3D Organic Animations http://www.chemtube3d.com

 Tel: +44 (0)151-794-3506 (3500 secretary)




 On 3 Oct 2008, at 00:06, [EMAIL PROTECTED] wrote:

 Message: 3
 Date: Thu, 2 Oct 2008 16:03:58 -0700
 From: Dean Johnston [EMAIL PROTECTED]
 Subject: Re: [Jmol-users] Creation / representation of aromatic bonds
 To: jmol-users@lists.sourceforge.net
 Message-ID:
 [EMAIL PROTECTED]
 Content-Type: text/plain; charset=iso-8859-1

 Have you tried 'calculate aromatic'?


 Regards,

 Rolf


 

 This message was sent using IMP, the Internet Messaging Program.



 Yes, but in my case that produces alternating double bonds and dashed
 single
 bonds - not a representation I've seen before.

 And I'm really looking for the proper set of connect commands that will
 give
 a conventional aromatic representation (all six carbon-carbon bonds with
 bond order 1.5, one solid bond and one dashed bond).

 Dean



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[Jmol-users] Translucent cylinder disappears when viewed edge on

[Dean Johnston]

Here's an odd one.  My (very short) translucent cylinders disappear when
viewed within a few degrees of edge-on.  To be more exact, the center
disappears while the edge remains visible.  These are the same type of
cylinders that are generated by the draw pointgroup command.  I've only
started to notice this with the most recent version (11.6.RC19).

Here's the command.

draw plane1_disk width 6.2001 cylinder {-0.0300 0. 0.} {0.0300
0. 0.} color translucent orange fixed;

Dean

P.S.  If it's any help, the angle at which it disappears gets smaller if you
turn on antialiasDisplay.
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[Jmol-users] Creation / representation of aromatic bonds

[Dean Johnston]

I don't know if this is a bug or a feature, but my script to display a model
of benzene ends up with all double bonds.  Here is a snippet of the script
(the structure is defined via an inline data file):

set autobond false;
data model benzene | ... (atom coordinates here) ... |end model benzene;
show data;
connect (atomno=1) (atomno=2) AROMATIC create;
connect (atomno=2) (atomno=3) AROMATIC create;
connect (atomno=3) (atomno=4) AROMATIC create;
connect (atomno=4) (atomno=5) AROMATIC create;
connect (atomno=5) (atomno=6) AROMATIC create;
connect (atomno=6) (atomno=1) AROMATIC create;

This produces all double bonds.  When I play around with the console, the
only way I can get what I want (and expect) is to say:

connect;
connect (atomno=1) (atomno=2) AROMATIC modify;
  ...etc. for all the remaining bonds

I've attached a state file.

Dean
# Jmol state version 11.6.RC17  2008-09-20 13:06;
  # fullName = jmolApplet0__18749094039234__;
  # documentBase = 
http://dhj-macbook.local/~djohnston/symmetry/tutorial/benzene.html;;
  # codeBase = http://dhj-macbook.local/~djohnston/symmetry/common/Jmol/;;


function _setWindowState();
# height 591;
# width 591;
  stateVersion = 1106000;
  backgroundColor = [xff];
  axis1Color = [xff];
  axis2Color = [x008000];
  axis3Color = [xff];
  ambientPercent = 45;
  diffusePercent = 84;
  specular = true;
  specularPercent = 22;
  specularPower = 40;
  specularExponent = 6;
  statusReporting  = true;
end function;

function _setFileState();

  set allowEmbeddedScripts false;
  set autoBond false;
  set appendNew true;
  set appletProxy ;
  set applySymmetryToBonds false;
  set bondRadiusMilliAngstroms 150;
  set bondTolerance 0.45;
  set defaultDirectory ;
  set defaultLattice {0.0 0.0 0.0};
  set defaultLoadScript ;
  set defaultVDW Jmol;
  set forceAutoBond false;
  set loadFormat http://www.rcsb.org/pdb/files/%FILE.pdb;;
  set minBondDistance 0.4;
  set pdbSequential false;
  set pdbGetHeader false;
  set percentVdwAtom 20;
  set smartAromatic true;
  data model inline
12
benzene
C   -1.2125   -0.70000.
C   -1.21250.70000.
C0.1.40000.
C1.21240.70000.
C1.2124   -0.70000.
C0.   -1.40000.
H   -2.1478   -1.24000.
H   -2.14781.24000.
H0.2.48000.
H2.14771.24000.
H2.1477   -1.24000.
H0.   -2.48000.
end model inline;;

end function;

function _setVariableState();

   set defaultanglelabel %VALUE %UNITS;
   set defaultcolorscheme Jmol;
   set defaultdirectory ;
   set defaultdistancelabel %VALUE %UNITS;
   set defaultdrawarrowscale 0.5;
   set defaultlattice {0 0 0};
   set defaultloadscript ;
   set defaulttorsionlabel %VALUE %UNITS;
   set defaulttranslucent 0.5;
   set defaultvdw Jmol;
  set allowembeddedscripts true;
  set allowrotateselected false;
  set appletproxy ;
  set applysymmetrytobonds false;
  set atompicking true;
  set autobond false;
  set autofps false;
  set axes window;
  set axesmode 0;
  set axesscale 2.0;
  set bondmodeor false;
  set bondpicking false;
  set bondradiusmilliangstroms 150;
  set bondtolerance 0.45;
  set cartoonrockets false;
  set chaincasesensitive false;
  set dataseparator ~~~;
  set delaymaximumms 0;
  set dipolescale 1.0;
  set disablepopupmenu false;
  set displaycellparameters true;
  set dotdensity 3;
  set dotsselectedonly false;
  set dotsurface true;
  set drawhover false;
  set drawpicking false;
  set dynamicmeasurements false;
  set ellipsoidarcs false;
  set ellipsoidaxes false;
  set ellipsoidaxisdiameter 0.02;
  set ellipsoidball true;
  set ellipsoiddotcount 200;
  set ellipsoiddots false;
  set ellipsoidfill false;
  set forceautobond false;
  set greyscalerendering false;
  set hbondsbackbone false;
  set hbondssolid false;
  set helppath http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm;;
  set hermitelevel 0;
  set hidenameinpopup false;
  set hidenavigationpoint false;
  set highresolution false;
  set historylevel 0;
  set hoverdelay 0.5;
  set isosurfacepropertysmoothing true;
  set justifymeasurements false;
  set loadformat http://www.rcsb.org/pdb/files/%FILE.pdb;;
  set measureallmodels false;
  set measurementlabels true;
  set messagestylechime false;
  set minbonddistance 0.4;
  set navigationperiodic false;
  set navigationspeed 5.0;
  set pdbgetheader false;
  set pdbsequential false;
  set percentvdwatom 20;
  set pickingspinrate 10;
  set picklabel ;
  set pointgroupdistancetolerance 0.2;
  set pointgrouplineartolerance 8.0;
  set propertyatomnumbercolumncount 0;
  set propertyatomnumberfield 0;
  set propertycolorscheme roygb;
  set propertydatacolumncount 0;
  set propertydatafield 0;
  set quaternionframe c;
  set rangeselected false;
  set ribbonaspectratio 16;
  set ribbonborder false;
  set rocketbarrels false;
  set selectallmodels true;
  set selecthetero true;
  set selecthydrogen true;
  set sheetsmoothing 1.0;

Re: [Jmol-users] Creation / representation of aromatic bonds

[Dean Johnston]

 Have you tried 'calculate aromatic'?

 Regards,
 Rolf

 
 This message was sent using IMP, the Internet Messaging Program.


Yes, but in my case that produces alternating double bonds and dashed single
bonds - not a representation I've seen before.

And I'm really looking for the proper set of connect commands that will give
a conventional aromatic representation (all six carbon-carbon bonds with
bond order 1.5, one solid bond and one dashed bond).

Dean
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[Jmol-users] State script not scaling arcs properly

[Dean Johnston]

Bob,

  I'm finding that my state script doesn't properly reproduce the scale of
the arcs.  They should be the same size as the disks (see the attached the
Jmol state file).  If this has been fixed since RC_12 then ignore this.

Dean
# Jmol state version 11.6.RC12_dev  2008-08-14 16:55;
  # fullName = jmolApplet0__9161665542644184__;
  # documentBase = http://dhj-macbook.local/~djohnston/symmetry/gallery3.html;;
  # codeBase = http://dhj-macbook.local/~djohnston/symmetry/gallery/Jmol/;;


function _setWindowState();
# height 586;
# width 586;
  stateVersion = 1106000;
  backgroundColor = [xff];
  axis1Color = [xff];
  axis2Color = [x008000];
  axis3Color = [xff];
  ambientPercent = 45;
  diffusePercent = 84;
  specular = true;
  specularPercent = 22;
  specularPower = 40;
  specularExponent = 6;
  statusReporting  = true;
end function;

function _setFileState();

  set allowEmbeddedScripts false;
  set autoBond false;
  set appendNew true;
  set appletProxy ;
  set applySymmetryToBonds false;
  set bondRadiusMilliAngstroms 150;
  set bondTolerance 0.45;
  set defaultDirectory ;
  set defaultLattice {0.0 0.0 0.0};
  set defaultLoadScript ;
  set defaultVDW Jmol;
  set forceAutoBond false;
  set loadFormat http://www.rcsb.org/pdb/files/%FILE.pdb;;
  set minBondDistance 0.4;
  set pdbSequential false;
  set pdbGetHeader false;
  set percentVdwAtom 20;
  set smartAromatic true;
  data model inline
22
bicyclo[2.2.2]octane
C0.   -1.44020.7646
C0.0.1.2819
C0.0001   -1.4403   -0.7645
C   -1.24720.72020.7646
C1.24740.72000.7646
C0.0.   -1.2819
C   -1.24730.7202   -0.7646
C1.24730.7200   -0.7646
H   -0.8821   -1.98151.1567
H0.   -1.98161.1567
H0.0.2.3959
H   -0.8820   -1.9815   -1.1567
H0.8818   -1.9816   -1.1566
H   -1.27501.75461.1567
H   -2.15700.22711.1567
H2.15700.22691.1567
H1.27521.75451.1567
H0.0.   -2.3960
H   -1.27511.7546   -1.1567
H   -2.15700.2271   -1.1567
H2.15700.2269   -1.1567
H1.27531.7544   -1.1567
end model inline;;

end function;

function _setVariableState();

   set defaultanglelabel %VALUE %UNITS;
   set defaultcolorscheme Jmol;
   set defaultdirectory ;
   set defaultdistancelabel %VALUE %UNITS;
   set defaultdrawarrowscale 0.5;
   set defaultlattice {0 0 0};
   set defaultloadscript ;
   set defaulttorsionlabel %VALUE %UNITS;
   set defaulttranslucent 0.5;
   set defaultvdw Jmol;
  set allowembeddedscripts true;
  set allowrotateselected false;
  set appletproxy ;
  set applysymmetrytobonds false;
  set autobond false;
  set autofps false;
  set axes window;
  set axesmode 0;
  set axesscale 2.0;
  set bondmodeor false;
  set bondradiusmilliangstroms 150;
  set bondtolerance 0.45;
  set cartoonrockets false;
  set chaincasesensitive false;
  set dataseparator ~~~;
  set delaymaximumms 0;
  set dipolescale 1.0;
  set disablepopupmenu false;
  set displaycellparameters true;
  set dotdensity 3;
  set dotsselectedonly false;
  set dotsurface true;
  set drawhover false;
  set drawpicking false;
  set dynamicmeasurements false;
  set ellipsoidarcs false;
  set ellipsoidaxes false;
  set ellipsoidaxisdiameter 0.02;
  set ellipsoidball true;
  set ellipsoiddotcount 200;
  set ellipsoiddots false;
  set ellipsoidfill false;
  set forceautobond false;
  set greyscalerendering false;
  set hbondsbackbone false;
  set hbondssolid false;
  set helppath http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm;;
  set hermitelevel 0;
  set hidenameinpopup false;
  set hidenavigationpoint false;
  set highresolution false;
  set historylevel 0;
  set hoverdelay 0.5;
  set isosurfacepropertysmoothing true;
  set justifymeasurements false;
  set loadformat http://www.rcsb.org/pdb/files/%FILE.pdb;;
  set measureallmodels false;
  set measurementlabels true;
  set messagestylechime false;
  set minbonddistance 0.4;
  set navigationperiodic false;
  set navigationspeed 5.0;
  set pdbgetheader false;
  set pdbsequential false;
  set percentvdwatom 20;
  set pickingspinrate 10;
  set picklabel ;
  set pointgroupdistancetolerance 0.2;
  set pointgrouplineartolerance 8.0;
  set propertyatomnumberfield 0;
  set propertycolorscheme roygb;
  set propertydatafield 0;
  set quaternionframe c;
  set rangeselected false;
  set ribbonaspectratio 16;
  set ribbonborder false;
  set rocketbarrels false;
  set selectallmodels true;
  set selecthetero true;
  set selecthydrogen true;
  set sheetsmoothing 1.0;
  set showhiddenselectionhalos false;
  set showhydrogens true;
  set showmeasurements true;
  set showmultiplebonds true;
  set shownavigationpointalways false;
  set smartaromatic true;
  set solventprobe false;
  set solventproberadius 1.2;
  set ssbondsbackbone false;
  set stereodegrees 5;
  set strandcountformeshribbon 7;
  set strandcountforstrands 5;
  set testflag1 false;
  set testflag2 false;

[Jmol-users] Behavior of the Jmol applet console output (on OS X)

[Dean Johnston]

Dear All,

Has anybody noticed a change in the console behavior for the applet between
RC12 and RC17?  I don't know if this is specific to OS X.  I used to be able
to select text from the applet console and drag it either to the desktop (to
create a text clipping) or to the console of the Jmol application.  (This
is a convenient way of checking if Jmol can reproduce any arbitrary applet
state.)

Now if I click in the applet console output text I can't do anything with
it.  The console also won't respond to select all (command-A) or other such
keyboard commands.  To me the console looks slightly different - different
font? - so I'm not sure what's changed.

System info:  Mac OS X 10.5.5, Jmol 11.6.RC17_dev, Java 1.5.0_13

Dean
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[Jmol-users] Best way to output results of script using Jmol application

[Dean Johnston]

Dear All,

  I've been playing around with some of the molecular math features of
Jmol - it's truly amazing how easy it is to analyze a large number of
structures.  My only difficulty has been getting the results out to a simple
text file.

At first I tried copying the text from the console - doesn't seem to work
(at least on OS X).

For simple scripts I was able to say:
output = script(echo hello world); write VAR output output.txt;

But this is cumbersome with longer scripts or with scripts that have quotes
in them.

The following seems to work (I just figured this out...):
output = script(script \myscript.spt\); write VAR output output.txt;

Am I missing an easier (cleaner?) way to do this?  I guess I'd like to be
able to tell the script(...) command that what is in the quotes is a path
to a file.

Just FYI, here is a bit of what I'm doing with this (the file is the results
of a search on the Cambridge Structure Database with about 100 structures).
The structures are all metal clusters and I'm calculating the average
distance from the center of the cluster to each of the bridging ligands in
the structure.  Pretty cool...

nModel = getProperty(modelInfo, modelCount);
for (x = 1; x = nModel; x = x+1);
name = getProperty(modelInfo, models, @x, name).trim(CSD_CIF);
model @x;
print Model # + x + :  + name;
bridging = (connected(3,{molybdenum})  {model = @x});
moly = ({molybdenum}  {model = @x});
print Bridging atoms:  + bridging.label(%e).join( );
print Bridging distance =  + bridging.distance(moly);
print ;
end for;
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Re: [Jmol-users] javascript command fails in Safari?

[Dean Johnston]

I can't reproduce this - the javascript command works just fine from the
Jmol console for me on both Firefox and Safari for OS X.

Dean

On Fri, Sep 5, 2008 at 6:18 PM, Eric Martz [EMAIL PROTECTED]wrote:

 It appears to me that the javascript command of Jmol does not work in
 Safari on Mac OS X.

 Examples, typed into the Jmol console:

 javascript alert(hi)
 or
 javascript alert(document.location.href)

 These display the alert in Firefox on Windows or Mac OS X, but not in
 Safari on Mac OS X.

 If this is a known limitation, I suggest that it be documented for
 the javascript command in the Jmol reference manual.

 Thanks, Eric


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Re: [Jmol-users] Testing 11.6.RC8

[Dean Johnston]

Bob,

  Jmol still seems to crash with write pointgroup draw on these three
examples (11.6.12_dev application): twistane, N2O4 and p-dibromobenzene.
Other examples of D2h symmetry also give the same problem.

Dean

On Wed, Aug 27, 2008 at 10:41 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 Dean, that fix is checked in -- problem for any case where there is no
 principal axis.



 On Fri, Aug 22, 2008 at 9:52 PM, Dean Johnston [EMAIL PROTECTED]wrote:

 OK, it's working much better, but a few obscure errors with my test set
 (this is with both 11.6.RC10-applet, and 11.6.RC11_dev-application).

 *D2* (twistane): correctly identifies point group, but crashes on write
 pointgroup draw
 *D2h* (N2O4): correctly identifies point group, but crashes on write
 pointgroup draw
 *D2h* (p-dibromobenzene): correctly identifies point group, but crashes
 on write pointgroup draw

 It must be a point group specific thing, because a lower symmetry (C2)
 version of my twistane structure works just fine.

 BTW, I love the getProperty pointGroupInfo.  Thanks Bob!

 Dean



 On Fri, Aug 22, 2008 at 10:01 AM, Robert Hanson [EMAIL PROTECTED]wrote:

 found it -- Nico, let's get RC10 out so Dean can test it.

 Bob



 On Thu, Aug 21, 2008 at 11:21 PM, Dean Johnston [EMAIL PROTECTED]wrote:

 This (the write pointgroup draw command) still isn't working for me
 (RC9 and RC10).  Not sure what is going on.

 Dean


 On Wed, Aug 20, 2008 at 2:18 AM, Robert Hanson [EMAIL PROTECTED]wrote:

 fixed and, sure, why not...

 getProperty pointGroupInfo

 print getProperty(pointgroupInfo.principalAxis)

 etc.


 On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]
  wrote:

 Bob,

 write pointgroup draw gives the following error (for 11.6.RC8):

 Exception in thread QueueThread0 java.lang.NullPointerException
 at org.jmol.symmetry.PointGroup.getInfo(Unknown Source)
 at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source)
 at
 org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown 
 Source)
 at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown
 Source)
 at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source)
 at org.jmol.viewer.Eval.write(Unknown Source)
 at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)...

 Unrelated question:  is there (or will there be) a getPropertycommand to 
 retrieve information about symmetry elements?  (I can grab them
 using show pointgroup, but getProperty would be nice).

 Dean


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


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

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

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Re: [Jmol-users] Echo with sub and sup tags

[Dean Johnston]

 measures 15.0 SansSerif Plain;
  select measures ({null});

  set echo off;
  set echo bottom left; echo Point Group = Csub3v/sub;
  font echo 15.0 SansSerif Italic; color echo [x808080];

  boundBox off;

  frank on;
  font frank 16.0 SansSerif Bold;
  set fontScaling false;

end function;

function _setPerspectiveState();
  set perspectiveModel 11;
  set scaleAngstromsPerInch 0.0;
  set perspectiveDepth false;
  set visualRange 5.0;
  set cameraDepth 3.0;
  boundbox corners {-0.47610003 -0.8247 -0.08415} {0.9522 0.8247 0.2525}
# volume = 0.7932107;
  center {0.0 0.0 -2.5004148E-5};
  moveto 0.0 { -983 160 90 73.64} 100.0 0.0 0.0 {0.0 0.0 -2.5004148E-5}
2.1559744 {0.0 0.0 0.0} 5.335241E-5 -5.513082E-4 50.0;;
  slab 100;depth 0;
  set spinX 0; set spinY 30; set spinZ 0; set spinFps 30;
end function;

function _setSelectionState();
  select ({0:3});
  set hideNotSelected false;
end function;

function _setState();
  initialize;
  set refreshing false;
  _setWindowState;
  _setFileState;
  _setVariableState;
  _setModelState;
  _setPerspectiveState;
  _setSelectionState;
  set refreshing true;
  set antialiasDisplay true;
  set antialiasTranslucent true;
  set antialiasImages true;
end function;

_setState;

On Wed, Aug 27, 2008 at 9:49 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 I'm not observing this, Dean. You will have to be more specific -- send a
 state script.

 Bob


 On Sun, Aug 24, 2008 at 9:10 PM, Dean Johnston [EMAIL PROTECTED]wrote:

 Dear All -

 I've just noticed an odd behavior with the echo command.  I've been using
 sub (subscript) tags in some of my echos (I think this is an undocumented
 feature).  At some recent point (after 11.4), any echo'ed text with a sub
 tag shows up with extra spaces between the letters.  All other echos are
 unaffected.  Has anybody else noticed this?  (Is anybody else using this
 feature?)

 Dean

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


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

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

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Re: [Jmol-users] problem in firefox

[Dean Johnston]

Jeff,

  No apologies needed.  Giving an id to a div does not create a Javascript
object automatically (at least in Firefox).  You will have to use something
like:

var myText = document.getElementById('jmolText');

and then say

myText.value = dump(_dataInfo);

It's interesting that it *does* work in Safari.

Dean


On Wed, Aug 27, 2008 at 11:05 AM, Jeff Hansen [EMAIL PROTECTED] wrote:

 My apologies.  This is really more of a javascript/html question but
 it is on a Jmol project I am working on.  Could someone explain to me
 what is the problem with the following code?  The appletReady()
 function works just fine in Safari and the page validates as HTML 4.01
 strict, but the appletReady() function doesn't work in Firefox.
 Firebug reports an error and says jmolText is not defined.

 function appletReady() {
 var _dataInfo = jmolGetPropertyAsArray(auxiliaryInfo);
 jmolText.value = dump(_dataInfo);
 }

 ...

 div id=textDiv
 form action=
 ptextarea cols=50 rows=50 id='jmolText'/textarea/p
 /form
 /div


 The page is at http://web.mac.com/jhansen4/Jmol/NewJmolDiv.html if
 that will help.


 ***
 Jeff Hansen
 Department of Chemistry and Biochemistry
 DePauw University
 602 S. College Ave.
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 ***



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Re: [Jmol-users] Echo with sub and sup tags

[Dean Johnston]

Found it!  It's an artifact of the set antialiasDisplay (true).  (It only
appears unusual when a sub or sup tag it present *and* antialiasDisplay
is on.)  I'll leave it to Bob to track *that* one down...

Dean

On Wed, Aug 27, 2008 at 11:56 AM, Angel Herráez [EMAIL PROTECTED]wrote:

 On 27 Aug 2008 at 10:57, Dean Johnston wrote:
  OK, here is the state for ammonia, with a label of Point Group =
 Csub3v/sub at the
  bottom left. Without the tags the spacing is normal.

 Just typing it in the console of 11.6.RC10 app it looks Ok to me
 Maybe some combination with other scripts are doing it?



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Re: [Jmol-users] Jmol-users Digest, getting data from Jmol

[Dean Johnston]

If you're using Firefox at all, I've found the Firebug plug-in (
http://getfirebug.com/) to be immensely useful.  Whether your debugging
Javascript or just want to look at the DOM, it works great for me.  Just set
a breakpoint right after your jmolGetPropertyAsArray() call and then find
your array over in the watch panel.

Dean

On Tue, Aug 26, 2008 at 4:48 PM, Jeff Hansen [EMAIL PROTECTED] wrote:

 Thanks Paul.  That is very helpful.  I was able to use it to display the
 data in the array in a text area on the web page.  Should prove useful for
 figuring out how to mine the data.

 ***
 Jeff Hansen
 Department of Chemistry and Biochemistry
 DePauw University
 602 S. College Ave.
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 ***


 On Aug 26, 2008, at 2:51 PM, Paul Pillot wrote:

 I use the following dump() script when I want a detailed content of an
 object/array in javascript :
 http://binnyva.blogspot.com/2005/10/dump-function-javascript-equivalent-of.html
 Paul

 Le 26 août 08 à 20:37, Jeff Hansen a écrit :

 I'm working with Spartan 04 .smol files.  I could use Spartan 06 files if
 necessary.
 I'm making progress.  I'm able to use jmolGetPropertyAsArray and pull a
 value out of that.  I would like to show the contents of the entire array so
 I could see what is there and how it is organized, but I'm having trouble
 figuring out how to do that.


 ***
 Jeff Hansen
 Department of Chemistry and Biochemistry
 DePauw University
 602 S. College Ave.
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 ***


 On Aug 26, 2008, at 12:41 PM, Robert Hanson wrote:

 The properties supported do depend upon the file type. What file type are
 you working with? Generally you can check this by using

 getproperty auxiliaryinfo

 which is a general holder for all sorts of molecular info.


 Bob


 On Mon, Aug 25, 2008 at 7:50 AM, Jeff Hansen [EMAIL PROTECTED] wrote:

 Bob,

 I've been looking through the documentation and trying to figure this out.
  I'm not having much success.  I don't think I quite understand the syntax
 for doing this.  I also don't understand what properties are available and
 where to find them and which file formats are supported.  I'm not finding
 the help I need in the documentation or at least I'm not understanding well
 enough the help that is there.  So lets say that I wanted to have a file
 with several related models and find the energy of the molecule in each
 model (actually that is what I want to do).  I'm not looking for the code to
 do this, just another pointer in the right direction to move me in the right
 direction.  Sorry if I'm too much of a bother.

 Robert Hanson
 Fri, 22 Aug 2008 07:22:24 -0700

 oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands
 include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or
 jmolGetPropertyAsString()


  ***
 Jeff Hansen
 Department of Chemistry and Biochemistry
 DePauw University
 602 S. College Ave.
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 ***



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 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] Echo with sub and sup tags

[Dean Johnston]

Dear All -

I've just noticed an odd behavior with the echo command.  I've been using
sub (subscript) tags in some of my echos (I think this is an undocumented
feature).  At some recent point (after 11.4), any echo'ed text with a sub
tag shows up with extra spaces between the letters.  All other echos are
unaffected.  Has anybody else noticed this?  (Is anybody else using this
feature?)

Dean
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[Jmol-users] Drawing individual symmetry elements

[Dean Johnston]

Dear All (but mostly Bob) -

(Sorry about the duplicate message regarding echo - I thought my mail
program never sent it out...)

I'm having problems drawing individual symmetry elements (Jmol 11.6.RC11)
using the format draw pointgroup c2 1

It correctly draws the first element, but then won't draw any other c2
axes.  For example:

draw delete; draw pointgroup c2 1; draw pointgroup c2 2  ---  only draws one
c2 axis

draw delete; draw pointgroup c2 1; draw delete; draw pointgroup c2 2 ---
draws the same c2 axis both times

but
draw delete; draw pointgroup c2 1; draw delete; draw pointgroup; draw
delete; draw pointgroup c2 2 --- correct draws two different c2 axes

I think this is recent, because the example on Bob's new pages (11.6.RC9)
works just fine, but the same molecule won't work with 11.6.RC11.  Can
anyone else reproduce this?

Dean
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Re: [Jmol-users] Jmol-users Digest, Vol 27, Issue 32

[Dean Johnston]

Jeff,

  You can certainly avoid using innerHTML.  I only ended up using it because
it was the only way to get my particular pages working with Internet
Explorer (arghh).  And now that I depend on it I don't bother to avoid it...

  In your almost working version, you were sending a Javascript object to
a function, newDiv.update(), that expected a string.  (The *new* keyword
returns a Javascript object.)  Javascript automatically converted your
jmolObject to a string -- object Object.  I've modified your code
slightly to something that I think should work (I can't really test it fully
here.)

Here's what I've done:
 - I've added an instance variable (this.loadString) to your jmolObject
(this lets me access the loadString later)
 - I've moved the jmolApplet command down so that the HTML string that is
returned by jmolApplet() is passed into the div.update()

It still feels a bit convoluted, but I hope it accomplishes what you want.

Dean

Modified code follows:
-
script type=text/javascript
   var jmolObject = Class.create();
   jmolObject.prototype = {
   initialize: function(molecule){
   jmolInitialize(jmol);
   jmolSetDocument(*false*);
   *this.loadString* = \load ../Jmol/jmol/models/ +
molecule + \;
   alert(this.loadString);
   }
   };
   var divInc = 0;
   function newJmolDiv(molecule) {
   var newDiv = document.createElement('div');
   var jmolID = 'jmolDiv_' + (divInc++);
   newDiv.id = jmolID;
   document.body.appendChild(newDiv);
   var myApplet = new jmolObject(molecule);
   *newDiv.update(jmolApplet(400, eval(myApplet.loadString)));*
   }
   function appletReady() {
   var atomSetArray =
jmolGetPropertyAsArray(atomInfo,atomno5);
   alert (atomSetArray[0].info);
   }
/script


On Sat, Aug 23, 2008 at 3:27 PM, Jeff Hansen [EMAIL PROTECTED] wrote:

 Dean,

 Many thanks.  I've got it working perfectly now.  The only tweak I had
 to make to your suggestion was to change loadString to
 eval(loadString).  From my reading I had thought that innerHTML was
 not part of the Standard and so I was trying not to use it.
 Interestingly my previous approach (creating a new jmol object) now
 works if I use eval(loadString) as long as I do not include the
 jmolSetDocument(false).  In this case it wipes the page and correctly
 displays the jmol applet.  When I add the jmolSetDocument(false) it
 writes [object Object] where the applet should be.  So the
 jmolSetDocument(false) is somehow messing up creating the jmol object
 correctly.  Dean, you were a great help.  Might someone help me figure
 out this other way too?  I would like to be as standards compliant as
 possible.

 Here is the current code that works (thanks Dean):
 script type=text/javascript
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
var jmolID = 'jmolDiv_' + (divInc++);
newDiv.id = jmolID;
document.body.appendChild(newDiv);
var loadString = \load ../Jmol/jmol/models/ + molecule +
 \;
jmolInitialize(jmol);
jmolSetDocument(false);
newDiv.innerHTML = jmolApplet(400, eval(loadString));
}
function appletReady() {
var atomSetArray =
 jmolGetPropertyAsArray(atomInfo,atomno5);
alert (atomSetArray[0].info);
}
 /script

 Here is the code that almost works.  Without jmolSetDocument(false) it
 clears the page and loads the applet.  With jmolSetDocument(false) it
 puts [object Object] in the new div.
 script type=text/javascript
var jmolObject = Class.create();
jmolObject.prototype = {
initialize: function(molecule){
jmolInitialize(jmol);
jmolSetDocument();
var loadString = \load ../Jmol/jmol/models/ +
 molecule + \;
alert(loadString);
jmolApplet(400, eval(loadString));
}
};
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
var jmolID = 'jmolDiv_' + (divInc++);
newDiv.id = jmolID;
document.body.appendChild(newDiv);
newDiv.update(new jmolObject(molecule));
}
function appletReady() {
var atomSetArray =
 jmolGetPropertyAsArray(atomInfo,atomno5);
alert (atomSetArray[0].info);
}
 /script



 ***
 Jeff Hansen
 Department of Chemistry and Biochemistry
 DePauw University
 602 S. College Ave.
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 

Re: [Jmol-users] Testing 11.6.RC8

[Dean Johnston]

OK, it's working much better, but a few obscure errors with my test set
(this is with both 11.6.RC10-applet, and 11.6.RC11_dev-application).

*D2* (twistane): correctly identifies point group, but crashes on write
pointgroup draw
*D2h* (N2O4): correctly identifies point group, but crashes on write
pointgroup draw
*D2h* (p-dibromobenzene): correctly identifies point group, but
crashes on write
pointgroup draw

It must be a point group specific thing, because a lower symmetry (C2)
version of my twistane structure works just fine.

BTW, I love the getProperty pointGroupInfo.  Thanks Bob!

Dean


On Fri, Aug 22, 2008 at 10:01 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 found it -- Nico, let's get RC10 out so Dean can test it.

 Bob



 On Thu, Aug 21, 2008 at 11:21 PM, Dean Johnston [EMAIL PROTECTED]wrote:

 This (the write pointgroup draw command) still isn't working for me (RC9
 and RC10).  Not sure what is going on.

 Dean


 On Wed, Aug 20, 2008 at 2:18 AM, Robert Hanson [EMAIL PROTECTED]wrote:

 fixed and, sure, why not...

 getProperty pointGroupInfo

 print getProperty(pointgroupInfo.principalAxis)

 etc.


 On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote:

 Bob,

 write pointgroup draw gives the following error (for 11.6.RC8):

 Exception in thread QueueThread0 java.lang.NullPointerException
 at org.jmol.symmetry.PointGroup.getInfo(Unknown Source)
 at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source)
 at
 org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown Source)
 at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source)
 at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source)
 at org.jmol.viewer.Eval.write(Unknown Source)
 at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)...

 Unrelated question:  is there (or will there be) a getProperty command
 to retrieve information about symmetry elements?  (I can grab them using 
 show
 pointgroup, but getProperty would be nice).

 Dean


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[Jmol-users] Echo with sub and sup tags

[Dean Johnston]

I've just noticed an odd behavior with the echo command.  I've been using
sub (subscript) tags in some of my echos (I think this is an undocumented
feature).  At some recent point (after 11.4), any echo'ed text with a sub
tag shows up with extra spaces between the letters.  All other echos are
unaffected.  Has anybody else noticed this?  (Is anybody else using this
feature?)

Dean
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Re: [Jmol-users] Testing 11.6.RC8

[Dean Johnston]

This (the write pointgroup draw command) still isn't working for me (RC9 and
RC10).  Not sure what is going on.

Dean

On Wed, Aug 20, 2008 at 2:18 AM, Robert Hanson [EMAIL PROTECTED] wrote:

 fixed and, sure, why not...

 getProperty pointGroupInfo

 print getProperty(pointgroupInfo.principalAxis)

 etc.


 On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote:

 Bob,

 write pointgroup draw gives the following error (for 11.6.RC8):

 Exception in thread QueueThread0 java.lang.NullPointerException
 at org.jmol.symmetry.PointGroup.getInfo(Unknown Source)
 at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source)
 at org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown
 Source)
 at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source)
 at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source)
 at org.jmol.viewer.Eval.write(Unknown Source)
 at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)...

 Unrelated question:  is there (or will there be) a getProperty command to
 retrieve information about symmetry elements?  (I can grab them using show
 pointgroup, but getProperty would be nice).

 Dean

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


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

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

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Re: [Jmol-users] script in string

[Dean Johnston]

I'm not sure of the context, but this should be OK if it's part of an *
external* javascript file.  If it's within an HTML page, the browser is
interpreting the /script in your string as the closing tag of your script,
thereby rendering everything that follows as HTML.

Dean

On Thu, Aug 21, 2008 at 11:20 PM, Jeff Hansen [EMAIL PROTECTED] wrote:

 Can anyone help me figure out what is wrong with this line of code?

var loadJmol = script
 type='text/javascript'addJmol(molecule,
 divInc);/script;

 What is happening is the /script is not being recognized or
 something and everything from the closing quotation mark on, including
 the next several lines until the next /script, is being displayed as
 text on the web page.


 ***
 Jeff Hansen
 Department of Chemistry and Biochemistry
 DePauw University
 602 S. College Ave.
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 ***



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Re: [Jmol-users] Testing 11.6.RC8

[Dean Johnston]

Bob,

write pointgroup draw gives the following error (for 11.6.RC8):

Exception in thread QueueThread0 java.lang.NullPointerException
at org.jmol.symmetry.PointGroup.getInfo(Unknown Source)
at org.jmol.symmetry.Symmetry.getPointGroupInfo(Unknown Source)
at org.jmol.modelset.ModelSet.calculatePointGroupForFirstModel(Unknown
Source)
at org.jmol.modelset.ModelSet.getPointGroupAsString(Unknown Source)
at org.jmol.viewer.Viewer.getPointGroupAsString(Unknown Source)
at org.jmol.viewer.Eval.write(Unknown Source)
at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)...

Unrelated question:  is there (or will there be) a getProperty command to
retrieve information about symmetry elements?  (I can grab them using show
pointgroup, but getProperty would be nice).

Dean
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Re: [Jmol-users] Jmol 11.6.RC3, point groups, dot density

[Dean Johnston]

On Fri, Aug 8, 2008 at 8:46 AM, Bob Hanson [EMAIL PROTECTED] wrote:

 version=11.6.RC3

 # bug fix: minor error in pointgroup
 # new feature: draw pointGroup [type] [index] SCALE [x]
 #  where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or
 the character n

 [Dean Johnston, please check that out]

 http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

Very nice - I like that you can select what to draw and the different color
for the horizontal plane.  How is the default scale determined? (It seems
with some molecules [C2h], the planes extend well beyond the outermost
atoms, while with others [Ih], they end in the middle of some atoms.)

Dean
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Re: [Jmol-users] Jmol 11.6.RC3, point groups, dot density

[Dean Johnston]

  Very nice - I like that you can select what to draw and the different
  color for the horizontal plane.  How is the default scale determined?
  (It seems with some molecules [C2h], the planes extend well beyond the
  outermost atoms, while with others [Ih], they end in the middle of
  some atoms.)
 
 right now it's just 3 Angstroms in diameter. I can't think of any
 general way to improve on that. Molecules come in all shapes and sizes,
 after all. I suppose it could be scaled based on the bounding box. Do
 you want me to try that?


Yes - I think planes should default to somewhat larger than the bounding box
- so that the atoms are completely within the circle.  Do the axes have the
same default?  I think they should be longer.

Dean
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Re: [Jmol-users] BCCE 2008 and Jmol

[Dean Johnston]

I will also be presenting at BCCE 2008.  While my materials
(http://symmetry.otterbein.edu) don't use all the latest and greatest that
Jmol has to offer, I will certainly sing its praises.  I'm looking forward
to some exciting sessions.

Dean Johnston


On 7/23/08 12:40 AM, Bob Hanson [EMAIL PROTECTED] wrote:

 Jonathan Gutow and I are both presenting Jmol-related talks at the
 Biennial Conference on Chemical Education, in Bloomington, Indiana, next
 week. I think I've asked this before, but I need to ask it again.
 
 My talk is entitled, What's New in Jmol.
 
 If you have utilized some of the newer capabilities of Jmol on public
 websites, please let me know so I can include references to your work in
 my presentation.
 
 Bob



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[Jmol-users] Jmol works on Safari 3.1 for Windows (!)

[Dean Johnston]

Jmol users,

  If anyone is interested, I just tried Jmol on Safari 3.1 for Windows
and it appears to work quite well.  (Previous versions of Safari for
Windows just hung up with many Java applets.)

  That said, I did find that some pages (in Bob's documentation examples
and Angel's pages) that I checked gave security exceptions and some
pages that dynamically resize the applet gave strange results.
FirstGlance appears to work.  I haven't checked a lot of other pages,
but my pages (with lots of Javascript) ran fine.  And the browser is
fast...

Dean


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[Jmol-users] Bug in Jmol menu - Select Element ?

[Dean Johnston]

I just noticed in the Jmol application that if I pick Select - Element
- (some element) from the pop-up menu, nothing gets selected.  The
console history shows that Jmol just sent the element name, not a
select (element) command.  For example, loading a structure and then
trying to select iron from the menu gives the following in the history:

vector 3
vector scale 1.0
vibration scale 0.5
vibration 0.5
load /home/djohnston/Structures and Plots/ferrocene.mol
console
iron#??

$ 

Should I submit a bug report on this?

Dean Johnston


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Re: [Jmol-users] new.htm updated

[Dean Johnston]

I can't reproduce this problem on my system (also OS X 10.4.11).  Jmol loads
just fine and all the example scripts appear to work.

Dean Johnston


On 11/28/07 3:44 AM, David Leader [EMAIL PROTECTED] wrote:

 Bob wrote:
 
 I've updated
 
 http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
 
 with the very latest for Jmol. Most notably:
 
 But on Mac 10.4.11 the applet on the page does not load using either
 Safari or Firefox (both latest versions) The Sun Java wait thingy
 just keeps going round with the progress bar about a quarter of the
 way along or less.
 
 No error messages in the console to give any clue what the problem is.
 
 My own jmol applets - somewhat older vintage - work ok.
 
 David
 
 
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Re: [Jmol-users] polyhedra files

[Dean Johnston]

Cool!  Very nicely done.

Dean


On 10/18/07 1:04 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 Robley Light wrote:
 
 Several weeks ago I asked the list if anyone knew of files that could
 display geometric shapes (for a lower grade math and science project).
 
 I'd like to thank Bob Hanson and Dean Johnston who not only put me on to a
 source of the xyz files but explained how to use Jmol.js to draw the edges
 and faces.
 
 In case anyone else is interested, I've posted these structures at
 http://chemweb.chem.fsu.edu/editors/rlight/polyhedra/index.html
 Feel free to use them. You can modify the spt files if you want to change
 the face colors.
  
 
 very nice!
 
 The tetrahedron needs a
 
   center *
 
 added to the script, I think.



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Re: [Jmol-users] Are there any files available displaying simple geometric solids

[Dean Johnston]

It's not a repository, but I do have a few of the structures you mention
(cube, octahedron, dodecahedron, icosahedron) on my site

http://symmetry.otterbein.edu/gallery/index.html

If you look closely (show history) you'll find they're constructed from
atoms (whatever was convenient) manually connected using the CONNECT
command.  The manual connections are required since they are not real
structures -- the default bonds that Jmol draws don't look too great.

As Bob suggests, you can use the DRAW command to draw faces.  The only
difficulty is faces with more than four sides.  For the dodecahedron my site
uses a combination of three-sided and four-sided figures to stitch
together a five-sided face.

I hope this is of some help.

Dean Johnston



On 9/6/07 5:55 PM, Robley Light [EMAIL PROTECTED] wrote:

 Its been a while since I've monitored this list, so forgive me if this is a
 question that has been asked and answered in the past.
 
 I'm working on a project related to some lower-grade math and science and I
 would like to use Jmol to display a variety of 3D solids (the five platonic
 ones, perhaps plus some other irregular ones).
 
 I can use ChemDraw to make a cube and tetrahedron of carbon atoms, save
 as a mol file, bring into Chem3D, delete the hydrogens, and
 minimize--producing a passable mol or pdb file for a cube and a
 tetrahedron.  I can probably spend some time trying to figure out the
 coordinate values to make the bonds longer, and I understand I can use
 Jmol.js commands to work on how to display these structures (still trying to
 learn that).
 
 Before trying to do this with more complex shapes, though, does anyone know
 of a repository of such geometric files that have already been created?
 (I've spent a couple of hours with Google with out success).  Or, does
 anyone have a suggestion of how to do this more easily (and elegantly)?
 
 Thanks.
 
 Robley Light
 
 *
 Robley J. Light Professor Emeritus of Chemistry and
 Biochemistry
 Department of Chemistry Phone:   (850) 644-3844
and Biochemistry   Email:  [EMAIL PROTECTED]
 95 Chieftan Way Fax:  (850) 644-8281
 Florida State University Home Page:
 http://www.chem.fsu.edu/editors/rlight
 Tallahassee, FL 32306-4390
  
 
 



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Re: [Jmol-users] Orient molecule along bond or arbitrary axis

[Dean Johnston]

OK, not simple, but very impressive what you can do with the molecular
math.  (I especially like the use of improper angles.)

Now, if I want to orient along an line (as opposed to along a bond), can I
do it the same way?  Is there a way to extract the endpoints of a line?
When I tried something like x = @line1.x I get what appears to be the center
point of the line instead of either end.  I guess I can always pass the
information to Jmol using Javascript, since that's how I created the line in
the first place.

Dean


On 6/15/07 12:58 AM, Bob Hanson [EMAIL PROTECTED] wrote:

 This is better -- it uses improper angles to set the sign of the angle
 correctly.
 
 Bob Hanson wrote:
 
 no simple way. HOWEVER, you could do the calculation I think. Let's see
 if it can be done with a Jmol script...
 
 Let's say we want to align the axis between atom 1 and atom 2 along the
 Z axis.
 
  Y
  |
  +--X
 /
Z
 
 Strategy: rotate the axis around the Z axis into the XZ plane, then
 rotate it around the Y axis into the YZ plane.
 To do this, we need two angles:
 
 a) the angle of the axis projected into the XY plane and the X axis,
 and, after that,
 b) the angle between the axis and the Z axis.
 
 try this:
 
  
 
 
 #atoms to align:
 
 a1 = 1
 a2 = 2
 
 # just for testing:
 
 select *;color cpk;
 select atomno=a1;color yellow;spacefill 0.40;
 select atomno=a2;color green;spacefill 0.25
 select atomno=a1 or atomno=a2; label on
 set axesmolecular
 axes on
 
 
 # align molecular and window frame coordinate system;
 
 reset
 select *
 
 
 # move atom 1 to {0 0 0}:
 
 x = -{atomno=a1}.x
 y = -{atomno=a1}.y
 z = -{atomno=a1}.z
 
 translateSelected [EMAIL PROTECTED] @y @z}
 
 # into the XZ plane, using an improper angle:
 
 axisAB = {atomno=a2}.xyz - {atomno=a1}.xyz
 
 x = axisAB.x
 y = axisAB.y
 #echo %{x} %{y}
 
 
 projAB = [EMAIL PROTECTED], @y, 0}
 angleA = angle(projAB, {0 0 0}, {0 0 1}, {1 0 0})
 #echo %{angleA}
 
 rotateSelected Z @angleA
 
 # move atom 1 to {0 0 0}:
 
 x = -{atomno=a1}.x
 y = -{atomno=a1}.y
 z = -{atomno=a1}.z
 
 translateSelected [EMAIL PROTECTED] @y @z}
 
 
 # onto the Z axis, using an improper angle:
 
 axisAB = {atomno=a2}.xyz - {atomno=a1}.xyz
 
 x = axisAB.x
 z = axisAB.z
 #echo %{x} %{z}
 
 projAB = [EMAIL PROTECTED], 0, @z}
 angleA = angle(projAB, {0 0 0}, {0 1 0}, {0 0 1})
 #echo %{angleA}
 
 rotateSelected Y @angleA
 
 # move atom 1 to {0 0 0}:
 
 x = -{atomno=a1}.x
 y = -{atomno=a1}.y
 z = -{atomno=a1}.z
 
 translateSelected [EMAIL PROTECTED] @y @z}
 
 
 
 Bob
 
 
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Re: [Jmol-users] Orient molecule along bond or arbitrary axis

[Dean Johnston]

Exactly.  I want to be able to look down a particular molecular axis - so
I guess that might be orient this bond along the Z axis.

Dean


On 6/14/07 10:45 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 Dean,
 
 There are two coordinate systems -- that of the molecule and that of the
 reference frame. Is what you are asking to do to align some axis in the
 molecular system with some axis in the reference plane? In other words,
 something like orient the axis going through atoms 1 and 2 along the X
 (horizontal) axis?
 
 
 Bob Hanson
 
 
 Dean Johnston wrote:
 
 Jmol users,
 
  Does anybody know a simple way to align a molecule in the Jmol viewer
 along a bond or (arbitrary) axis?  This axis may not correspond to one of
 the original x, y, or z axes.  (or front, back, top, etc.)   I know you can
 ROTATE around an arbitrary axis.   I also know you can also NAVIGATE along a
 PATH, but I just want to re-orient, not move anywhere.  Am I overlooking
 some obvious parameter to MOVETO?  Thanks for any tips.
 
 Dean
..



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Re: [Jmol-users] Polyhedra with 12 or 20 vertices

[Dean Johnston]

OK, I see that the POLYHEDRA command is really overkill for what I'm trying
to do.  I could essentially create my own polyhedral representations if the
DRAW command was extended to allow the drawing of planes with an arbitrary
number of vertices so that I could create triangles, pentagons, etc. as
needed.  Should I submit this as a feature request???

Dean


On 6/9/07 12:51 AM, Bob Hanson [EMAIL PROTECTED] wrote:

 Dean, sounds like you might appreciate:
 http://www.scienceu.com/geometry/facts/solids/coords/
 
 Well, ah, let's just say it doesn't work the way you probably think it
 does. The polyhedra code is a very complex algorithm that looks at
 possible faces (combinations of three atoms around a central atom) and
 determines which are faces and which are not. We have:
 
 #atoms comb of 3 at a time
 4 4!/(3!)(1!) = 4
 6 6!/3!3! = 20
 8 8!/3!5! = 56
 9 9!/3!6! = 84
 12 12!/3!9! = 220
 20 20!/3!17! = 1140
 ...
 n n(n-1)(n-2)/6
 
 so if you do nothing special, then you will possibly run into the
 problem with any number more than 9. HOWEVER, the algorithm has a
 parameter, distanceFactor, that is adjustable, and if you set it
 smaller, it will work. For example (That second line should not wrap), try:
 
 13
 #jmolscript: connect (*) (*) delete;connect (_Fe) (_C);select
 *;wireframe off;spacefill off;select (_Fe); polyhedra bonds
 distanceFactor 0.5
 Fe 0 0 0
 C -0.692 0.000 0.427
 C 0.000 0.427 -0.692
 C 0.000 0.427 0.692
 C 0.692 0.000 -0.427
 C -0.427 -0.692 0.000
 C -0.427 0.692 0.000
 C 0.000 -0.427 0.692
 C 0.427 0.692 0.000
 C 0.000 -0.427 -0.692
 C 0.692 0.000 0.427
 C 0.427 -0.692 0.000
 C -0.692 0.000 -0.427
 
 As for dodecahedra, that's just too large. I've upped the maximum number
 of faces to 147, and that takes care of it, but there are a few stray
 lines, since we are painting more triangles than actually needed. Just
 the way it goes, I guess
 
 
 
 Bob

 
 
 Dean Johnston wrote:
 
 Has anybody tried to create polyhedra with 12 or 20 vertices? The
 documentation seems to indicate that I should be able to go up to 20.
 
 I¹m creating representations of shapes (Platonic solids, actually ‹
 maybe Jmol isn¹t just for molecules anymore... :-). I would like to
 display an icosahedron and dodecahedron. I¹ve created structures with
 a central atom surrounded by 12 or 20 atoms, but when I try and create
 the polyhedron, I get the following error message:
 
 Polyhedron error: maximum face(87) -- reduce RADIUS
 
 I have a feeling it¹s creating more polyhedra faces than I want it to
 (I only want 20), but I¹m not entirely familiar with how it works.
 I¹ve gotten it to work just fine for tetrahedra and octahedra. Any
 insights, corrections, etc. are greatly appreciated.
 
 My testing page is at:
 http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/poly.html
 
 Dean
 
 
 
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Re: [Jmol-users] The future of Java?

[Dean Johnston]

I could get some relatively simple Java applets to run on Safari/WinXP, but
not Jmol.  All the reports I've read say Safari on Windows is pretty
unstable, but I don't know what Java support it's supposed to have.

Dean


On 6/13/07 2:51 PM, Alan Hewat [EMAIL PROTECTED] wrote:

 Jobs also confirmed that iPhone won't support Java.
 
 Does even Safari for Windows support Java ? I couldn't get jmol to work
 with Safari on my Windows-XP ThinkPad and Safari wouldn't run at all on my
 old Win-2000 Dell. If you think that i-phone is important, or any of the
 other i-marketing gadgets for that matter, don't miss the i-rack YouTube
 clip http://www.youtube.com/watch?v=AGHty_S0TU0
 No exit stategy ? Wait until you see our next product, i-ran.
 _
 Dr Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED]fax+33.476.20.76.48
 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/
 _



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Re: [Jmol-users] Polyhedra with 12 or 20 vertices

[Dean Johnston]

On 6/13/07 12:38 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 Yes, but don't hold your breath. It isn't core Jmol to be drawing random
 objects. If you really want to do it with Jmol, think about ways you can
 do it yourself with Jmol and triangles/quadrilaterals, and you will get
 there faster. You can load a file of coordinates and work with it to
 draw just about anything you want, provided the objects are triangles or
 quadrilaterals. Pmesh is another command that comes to mind.
 
 Bob
  Triangles and quadrilaterals will do just fine - for some reason I had the
PLANE keyword in my DRAW commands, so I forgot that triangles were that
easy.  Thanks!

Dean



 Dean Johnston wrote:
 
 OK, I see that the POLYHEDRA command is really overkill for what I'm trying
 to do.  I could essentially create my own polyhedral representations if the
 DRAW command was extended to allow the drawing of planes with an arbitrary
 number of vertices so that I could create triangles, pentagons, etc. as
 needed.  Should I submit this as a feature request???



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[Jmol-users] Jmol applet - crash with inline model (OS X)

[Dean Johnston]

I¹m getting an odd (and hard to reproduce) crash with the Jmol applet
(Firefox or Safari on OS X, version 11.1.48_dev).  I try and load an inline
model and sporadically get the error listed below.  It seems to always be in
the middle of creating the new bonds (my page creates all the bonds manually
from a connection list) after the molecule loads.

For some reason I never get the same error under Windows (Firefox or IE).

If it¹s any help, my earlier version of the page that uses the 11.1.22
applet does not produce the same error.

Dean Johnston

---
FileManager.openStringInline()
The Resolver thinks Xyz
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty modelInfo or getProperty
auxiliaryInfo to inspect them.
ModelSet: autobonding; use  autobond=false  to not generate bonds
automatically
data model molecule
|12|molecule|C   -1.2125   -0.70000.|C   -1.21250.7000
0.|C0.1.40000.|C1.21240.70000.|C
1.2124   -0.70000.|C0.   -1.40000.|H   -2.1478
-1.24000.|H   -2.14781.24000.|H0.2.4800
0.|H2.14771.24000.|H2.1477   -1.24000.|H
0.   -2.48000.|
12 bonds deleted
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
Exception in thread AWT-EventQueue-8 java.lang.NullPointerException
at org.jmol.shape.Sticks.setModelClickability(Unknown Source)
at org.jmol.modelset.ModelSet.setModelVisibility(Unknown Source)
at org.jmol.modelset.ModelManager.setModelVisibility(Unknown Source)
at org.jmol.viewer.Viewer.setModelVisibility(Unknown Source)
at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
at org.jmol.applet.Jmol.update(Unknown Source)
at org.jmol.applet.Jmol.update(Unknown Source)
at org.jmol.appletwrapper.AppletWrapper.update(Unknown Source)
at sun.awt.RepaintArea.updateComponent(RepaintArea.java:267)
at sun.awt.RepaintArea.paint(RepaintArea.java:233)
at apple.awt.ComponentModel.handleEvent(ComponentModel.java:251)
at apple.awt.MyCPanel.handleEvent(MyCPanel.java:97)
at java.awt.Component.dispatchEventImpl(Component.java:4097)
at java.awt.Container.dispatchEventImpl(Container.java:2068)
at java.awt.Component.dispatchEvent(Component.java:3869)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
at jep.MySimpleEventQueue.dispatchEvent(MySimpleEventQueue.java:59)
at 
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
va:269)
at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:190)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
1 new bonds; 0 modified
perspectivedepth = false
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Re: [Jmol-users] Jmol applet - crash with inline model (OS X)

[Dean Johnston]

Bob,

  Here's the script that produced the error in my previous message:

data model molecule|12|molecule|C   -1.2125   -0.70000.|C
-1.21250.70000.|C0.1.40000.|C1.2124
0.70000.|C1.2124   -0.70000.|C0.   -1.4000
0.|H   -2.1478   -1.24000.|H   -2.14781.24000.|H
0.2.48000.|H2.14771.24000.|H2.1477
-1.24000.|H0.   -2.48000.|end model molecule;show
data;
connect (all) (all) delete; connect (atomno=001) (atomno=002 ) AROMATIC
create;connect (atomno=002) (atomno=003 ) AROMATIC create;connect
(atomno=003) (atomno=004 ) AROMATIC create;connect (atomno=004) (atomno=005
) AROMATIC create;connect (atomno=005) (atomno=006 ) AROMATIC create;connect
(atomno=006) (atomno=001 ) AROMATIC create;connect (atomno=001) (atomno=007
) SINGLE create;connect (atomno=002) (atomno=008 ) SINGLE create;connect
(atomno=003) (atomno=009 ) SINGLE create;connect (atomno=004) (atomno=010 )
SINGLE create;connect (atomno=005) (atomno=011 ) SINGLE create;connect
(atomno=006) (atomno=012 ) SINGLE create;
set perspectiveDepth off; center all
set echo bottom left; font echo 15 sansserif italic; color echo gray; echo
Point Group = D6h

  As I said before, however, I can only produce the error sporadically and
only on OS X.  In general I can load several molecules successfully before I
get this error.  It doesn't seem to be a memory issue, however.  Let me know
if you want me to put up an example page (it's currently just running
locally).

Dean


On 6/8/07 10:39 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 Dean, please send me the script. I'd like to fix this.
 
 Dean Johnston wrote:
 
 I¹m getting an odd (and hard to reproduce) crash with the Jmol applet
 (Firefox or Safari on OS X, version 11.1.48_dev). I try and load an
 inline model and sporadically get the error listed below. It seems to
 always be in the middle of creating the new bonds (my page creates all
 the bonds manually from a connection list) after the molecule loads.
 
 For some reason I never get the same error under Windows (Firefox or IE).
 
 If it¹s any help, my earlier version of the page that uses the 11.1.22
 applet does not produce the same error.
 
 Dean Johnston
 
 ---
 FileManager.openStringInline()
 The Resolver thinks Xyz
 ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
 1 model in this collection. Use getProperty modelInfo or getProperty
 auxiliaryInfo to inspect them.
 ModelSet: autobonding; use autobond=false to not generate bonds
 automatically
 data model molecule
 |12|molecule|C -1.2125 -0.7000 0.|C -1.2125 0.7000 0.|C 0.
 1.4000 0.|C 1.2124 0.7000 0.|C 1.2124 -0.7000 0.|C 0.
 -1.4000 0.|H -2.1478 -1.2400 0.|H -2.1478 1.2400 0.|H
 0. 2.4800 0.|H 2.1477 1.2400 0.|H 2.1477 -1.2400 0.|H
 0. -2.4800 0.|
 12 bonds deleted
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 Exception in thread AWT-EventQueue-8 java.lang.NullPointerException
 at org.jmol.shape.Sticks.setModelClickability(Unknown Source)
 at org.jmol.modelset.ModelSet.setModelVisibility(Unknown Source)
 at org.jmol.modelset.ModelManager.setModelVisibility(Unknown Source)
 at org.jmol.viewer.Viewer.setModelVisibility(Unknown Source)
 at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
 at org.jmol.applet.Jmol.update(Unknown Source)
 at org.jmol.applet.Jmol.update(Unknown Source)
 at org.jmol.appletwrapper.AppletWrapper.update(Unknown Source)
 at sun.awt.RepaintArea.updateComponent(RepaintArea.java:267)
 at sun.awt.RepaintArea.paint(RepaintArea.java:233)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:251)
 at apple.awt.MyCPanel.handleEvent(MyCPanel.java:97)
 at java.awt.Component.dispatchEventImpl(Component.java:4097)
 at java.awt.Container.dispatchEventImpl(Container.java:2068)
 at java.awt.Component.dispatchEvent(Component.java:3869)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
 at jep.MySimpleEventQueue.dispatchEvent(MySimpleEventQueue.java:59)
 at 
 java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.jav
 a:269)
 at 
 java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:
 190)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 perspectivedepth = false
 
 
 
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[Jmol-users] Polyhedra with 12 or 20 vertices

[Dean Johnston]

Has anybody tried to create polyhedra with 12 or 20 vertices?  The
documentation seems to indicate that I should be able to go up to 20.

I¹m creating representations of shapes (Platonic solids, actually ‹ maybe
Jmol isn¹t just for molecules anymore...  :-). I would like to display an
icosahedron and dodecahedron.  I¹ve created structures with a central atom
surrounded by 12 or 20 atoms, but when I try and create the polyhedron, I
get the following error message:

  Polyhedron error: maximum face(87) -- reduce RADIUS

I have a feeling it¹s creating more polyhedra faces than I want it to (I
only want 20), but I¹m not entirely familiar with how it works.  I¹ve gotten
it to work just fine for tetrahedra and octahedra.  Any insights,
corrections, etc. are greatly appreciated.

My testing page is at:
http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/poly.html

Dean
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Re: [Jmol-users] Jmol applet - crash with inline model (OS X)

[Dean Johnston]

Beautiful - explained the problem AND fixed the problem AND removed some
extraneous scripting to boot.  All in one step.  THANKS!

Dean


On 6/8/07 11:33 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 I think this system uses multiple threads, and the first thread has hit:
 
 connect (all) (all) delete;
 
 and is in the process of deleting the bonds when another thread starts
 rendering the picture. So the first thread has cleared some bonds that
 the renderer thread needs.
 I'll look into it.
 
 You might consider instead of the above to
 
 set autobond false
 data .
 
 Then there is less chance of such a thing happening.
 
 Bob
 
 
 connect (atomno=001) (atomno=002 ) AROMATIC
 create;connect (atomno=002) (atomno=003 ) AROMATIC create;connect
 (atomno=003) (atomno=004 ) AROMATIC create;connect (atomno=004) (atomno=005
 ) AROMATIC create;connect (atomno=005) (atomno=006 ) AROMATIC create;connect
 (atomno=006) (atomno=001 ) AROMATIC create;connect (atomno=001) (atomno=007
 ) SINGLE create;connect (atomno=002) (atomno=008 ) SINGLE create;connect
 (atomno=003) (atomno=009 ) SINGLE create;connect (atomno=004) (atomno=010 )
 SINGLE create;connect (atomno=005) (atomno=011 ) SINGLE create;connect
 (atomno=006) (atomno=012 ) SINGLE create;
 set perspectiveDepth off; center all
 set echo bottom left; font echo 15 sansserif italic; color echo gray; echo
 Point Group = D6h
 
  As I said before, however, I can only produce the error sporadically and
 only on OS X.  In general I can load several molecules successfully before I
 get this error.  It doesn't seem to be a memory issue, however.  Let me know
 if you want me to put up an example page (it's currently just running
 locally).
 
 Dean
 
 
 On 6/8/07 10:39 PM, Bob Hanson [EMAIL PROTECTED] wrote:
 
  
 
 Dean, please send me the script. I'd like to fix this.
 
 Dean Johnston wrote:
 

 
 I¹m getting an odd (and hard to reproduce) crash with the Jmol applet
 (Firefox or Safari on OS X, version 11.1.48_dev). I try and load an
 inline model and sporadically get the error listed below. It seems to
 always be in the middle of creating the new bonds (my page creates all
 the bonds manually from a connection list) after the molecule loads.
 
 For some reason I never get the same error under Windows (Firefox or IE).
 
 If it¹s any help, my earlier version of the page that uses the 11.1.22
 applet does not produce the same error.
 
 Dean Johnston
 
 ---
 FileManager.openStringInline()
 The Resolver thinks Xyz
 ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
 1 model in this collection. Use getProperty modelInfo or getProperty
 auxiliaryInfo to inspect them.
 ModelSet: autobonding; use autobond=false to not generate bonds
 automatically
 data model molecule
 |12|molecule|C -1.2125 -0.7000 0.|C -1.2125 0.7000 0.|C 0.
 1.4000 0.|C 1.2124 0.7000 0.|C 1.2124 -0.7000 0.|C 0.
 -1.4000 0.|H -2.1478 -1.2400 0.|H -2.1478 1.2400 0.|H
 0. 2.4800 0.|H 2.1477 1.2400 0.|H 2.1477 -1.2400 0.|H
 0. -2.4800 0.|
 12 bonds deleted
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 Exception in thread AWT-EventQueue-8 java.lang.NullPointerException
 at org.jmol.shape.Sticks.setModelClickability(Unknown Source)
 at org.jmol.modelset.ModelSet.setModelVisibility(Unknown Source)
 at org.jmol.modelset.ModelManager.setModelVisibility(Unknown Source)
 at org.jmol.viewer.Viewer.setModelVisibility(Unknown Source)
 at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
 at org.jmol.applet.Jmol.update(Unknown Source)
 at org.jmol.applet.Jmol.update(Unknown Source)
 at org.jmol.appletwrapper.AppletWrapper.update(Unknown Source)
 at sun.awt.RepaintArea.updateComponent(RepaintArea.java:267)
 at sun.awt.RepaintArea.paint(RepaintArea.java:233)
 at apple.awt.ComponentModel.handleEvent(ComponentModel.java:251)
 at apple.awt.MyCPanel.handleEvent(MyCPanel.java:97)
 at java.awt.Component.dispatchEventImpl(Component.java:4097)
 at java.awt.Container.dispatchEventImpl(Container.java:2068)
 at java.awt.Component.dispatchEvent(Component.java:3869)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
 at jep.MySimpleEventQueue.dispatchEvent(MySimpleEventQueue.java:59)
 at 
 java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.j
 av
 a:269)
 at 
 java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.jav
 a:
 190)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 1 new bonds; 0 modified
 perspectivedepth = false

Re: [Jmol-users] problem with old tutorial (and inline data)

[Dean Johnston]

I had similar problems - On OS X the Java cache is located in
~/Library/Caches/Java/cache ­ you can clear it using the Java Preferences
utility.  I always wondered why clearing the browser cache didn¹t always
work when I updated Jmol versions.

Unrelated note ­ has anybody tried inline files using the DATA command?  I¹m
getting the following error:

FileManager.openStringInline()
file ERROR: string
unrecognized file format for file string

It doesn¹t work with my site or with any of the examples in the Jmol doc.

Dean




On 5/18/07 10:06 AM, Sérgio Ceroni da Silva [EMAIL PROTECTED] wrote:

 Bob Hanson escreveu:
  
 I think it's a level of change none of us understand -- the cache I was
 referring to was the Java cache, which is where the JAR files go, which
 is different (sigh) from the browser cache; apparently that was not
 cleared. I've seen it happen, but I don't know exactly how to remedy it.
 Shouldn't be a major issue. Somehow the Java Virtual Machine gets messed
 up and tries to read the wrong set of JAR files.
 
 Bob
 In WinXP this cache is located in C:\Documents and
 Settings\USERNAME\Application data\Sun\Java\Deployment\cache and can be
 cleared through StartControl PanelJavaGeneralSettings. I've run into
 trouble with some java applications before (never with Jmol) and developed the
 habit of clearing this cache periodically.
 Regards
 Sérgio
 
 
 
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Re: [Jmol-users] Set backgroundModel in Jmol 11.1.22

[Dean Johnston]

You're right Bob, some of my scripts were using the simple integer notation
and causing the problem.  Works just fine now.  Thanks.

Dean


On 3/20/07 2:26 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 I think your problem is using simple integers like 1,2,3 in these more
 complicated situations. Make sure you specify the background model
 using the file.model convention -- 1.1 for the first model in the
 first file, 1.2, for the second model in the first file, 2.1 for the
 first model in the second file, etc.
 
 This worked for me on the following test:
 load =1crn
 data append
 2
 test
 C 0 0 0
 O 1 1 1
 2
 test
 N 2 0 0
 O 2 1 1
  end append;
 
 backgroundModel = 1.1
 frame 2.1
 frame 2.2
 
 etc.
 
 The two appended models are in the same file because XYZ files allow
 for multiple models. If you use a data separator between the models,
 like this:
 
 load 1.pdb
 dataSeparator = -\n
 data append
 2
 test
 C 0 0 0
 O 1 1 1
 -
 2
 test
 N 2 0 0
 O 2 1 1
  end append;
 
 then the two data sets can be any format (not necessarily the same),
 and they will end up in two separate files. After this we would have
 three models and three files:
 
 1.1  1crn
 2.1  CO
 3.1  NO
 
 Bob
 
 
 On 3/18/07, Dean Johnston [EMAIL PROTECTED] wrote:
   I can't seem to get set backgroundModel n to work when loading files
 using the inline append command with Jmol 11.1.22.  It works just fine with
 the normal (non appended) inline files.  Has anyone else tried this with
 appended file sets?
 
   On a related note, show backgroundModel always says backgroundmodel =
 not set whether it has been set or not.
 
 Dean
 
 
 
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Re: [Jmol-users] Jmol 11.1.22

[Dean Johnston]

 Similarly,
 
 data append .end append ;
 
 will insert an inline model into either a new frame or the current
 frame, as per the setting of appendNew.
  Is it possible to insert more than one new model using data append ?
When I try I get the following:

Exception in thread Thread-203 java.lang.ArrayIndexOutOfBoundsException: 1
at org.jmol.viewer.Mmset.setModelNameNumberProperties(Mmset.java:269)
at org.jmol.viewer.Frame.initializeModel(Frame.java:263)
at org.jmol.viewer.Frame.init(Frame.java:143)
at org.jmol.viewer.ModelManager.merge(ModelManager.java:80)
at org.jmol.viewer.Viewer.getOpenFileError(Viewer.java:1468)
at org.jmol.viewer.Viewer.openStringInline(Viewer.java:1337)
at org.jmol.viewer.Viewer.loadInline(Viewer.java:1396)
...

Dean



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Re: [Jmol-users] Jmol 11.1.21 -- numerical translucency

[Dean Johnston]

Bob,

  Are you saying we should ask for too much more often?  ;-)

  I LOVE the translucency - I've been playing around with it using the
application - it's exactly what I was thinking of and makes isosurfaces so
much nicer.  I guess it's not yet in the applet?  (You mention version
11.1.21 and I'm building 11.1.20).

The applet gives the following error:

Exception in thread Thread-45 java.lang.NoSuchFieldError: translucentLevel
at org.jmol.viewer.MeshCollection.setProperty(MeshCollection.java:164)
at org.jmol.viewer.Draw.setProperty(Draw.java:252)
at org.jmol.viewer.Frame.setShapeProperty(Frame.java:1180)
Etc...


On 3/13/07 6:44 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 Just cleaning house. Dean, I hope you get this message and take a look
 at 11.1.21.
 
 color xxx translucent 1
 
 through
 
 color xxx translucent 6
 
 
 Bob
 
 Dean wrote:
 
 I know this is probably too much to ask, but is there any way to make
 translucent objects show up through other translucent objects?  For
 example,  
 if I draw a translucent plane, any translucent atoms that move behind the
 plane just disappear as if the plane is opaque.  It sort of destroys the
 illusion of translucency.  I have a simple (very artificial) example
 page at  
 http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/trans_test.html.  In
 http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/trans_test.html.%C2%A0%C2%
 A0In 
 that  
 example, the oxygen and the plane are translucent and the hydrogens are
 opaque -- but you can't see the oxygen through the translucent plane.
  
 Dean Johnston 
 
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Re: [Jmol-users] Jmol 11.1.21 -- numerical translucency

[Dean Johnston]

I got it now - works great.  The ability to fade in is an especially nice
effect.

Dean

On 3/13/07 10:05 PM, Dean Johnston [EMAIL PROTECTED] wrote:

 Bob,
 
   Are you saying we should ask for too much more often?  ;-)
 
   I LOVE the translucency - I've been playing around with it using the
 application - it's exactly what I was thinking of and makes isosurfaces so
 much nicer.  I guess it's not yet in the applet?  (You mention version
 11.1.21 and I'm building 11.1.20).
 
 The applet gives the following error:
 
 Exception in thread Thread-45 java.lang.NoSuchFieldError: translucentLevel
 at org.jmol.viewer.MeshCollection.setProperty(MeshCollection.java:164)
 at org.jmol.viewer.Draw.setProperty(Draw.java:252)
 at org.jmol.viewer.Frame.setShapeProperty(Frame.java:1180)
 Etc...
 
 
 On 3/13/07 6:44 PM, Bob Hanson [EMAIL PROTECTED] wrote:
 
 Just cleaning house. Dean, I hope you get this message and take a look
 at 11.1.21.
 
 color xxx translucent 1
 
 through
 
 color xxx translucent 6
 
 
 Bob



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Re: [Jmol-users] Is there a simple way to create an ellipse?

[Dean Johnston]

On 3/7/07 4:17 AM, Angel Herraez [EMAIL PROTECTED] wrote:

 A flat ellipsoid?
 I wouldn't call that easy, but...
  That doesn't really work because isn't a flat ellipsoid (large
eccentricity) just a circle?  And you can't really get it totally flat.

 You can also create a polygon with as many vertices as you are
 willing to calculate.
  Can you do this with the draw command?  All I can get is lines (two
points), triangles (three points), and four-sided figures.  It seems to
ignore any points beyond four.  I guess I could create an inline pmesh, but
that definitely is not easy...

Dean



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[Jmol-users] Is there a simple way to create an ellipse?

[Dean Johnston]

Jmol users,

  I¹d like to create a representation of a plane that is an ellipse rather
than a rectangle.  Is there a simple way to create a representation of an
ellipse in Jmol?  Thanks for any pointers / suggestions.

Dean Johnston
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Re: [Jmol-users] Cell blocks available with mol2 formatted files?

[Dean Johnston]

Aidan,

I don't know if this helps, but when I type show spacegroup from the
console for your mol2 file, it says could not identify space group from
name: 14 1.  (The pdb file shows the correct spacegroup, P 21/c, and 14
does correspond to P 21/c)

I think this is a bug.  Looking at the code it looks like
Mol2Reader.readCrystalInfo must be reading 14  1 instead of just 14.
Should be a simple fix.  Bob?

Dean Johnston



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Re: [Jmol-users] Jmol 11.1.13 feature PROPOSAL

[Dean Johnston]

 I have just checked in a version of Jmol that allows:
 inverting selected atoms about points and planes
  I like it!  I thought about asking to add something like this a while
back, but never got around to submitting an official feature request.  I can
think of some really nice ways of using this capability.  (I'm working on
some pages that illustrate concepts of point-group symmetry - see
http://www.otterbein.edu/home/fac/dnhjhns/xmltest/demo.html )  I still
haven't had time to digest the cool new scripting capabilities...

 And, yes, I know -- the next thing needed is rotateSelected. I'm
 working on that.
  Any chance you can think about improper rotations as well?  :-)

 Comments? Suggestions for perhaps a SIMPLE general format for writing
 coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited,
 but with bonds), PDB? (unlimited, but rather involved).
 
 Alternatively, should Jmol have a new native format that includes the
 state?
  If Jmol is creating it, what you have looks ok (except for connectivity).
I don't know if bonds should be stored like MOL files or as Jmol commands
(like the state).  I like the idea (in principle) of using XML, though it
certainly doesn't fit the simple criterion.

Dean


On 2/14/07 7:01 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 I have just checked in a version of Jmol that allows:
 
 inverting selected atoms about points and planes
 
 writing of selected coordinates and orientation
 reading those files back into Jmol
 
 
 
 Basically, there is a new command:
 
invertSelection
 
 which by itself inverts all atoms through the center of rotation
 
invertSelection POINT [some point description]
 
 which inverts selected atoms through a point
 
invertSelection PLANE [some plane description]
 
 which inverts selected atoms across a plane
 
 Now, once this is done, of course, the atoms are not where they used to
 be. That would mess up the state, so I have added a new DATA type called
 coord:
 
 DATA coord set
 24 ;
 Jmol Coordinate Data Format 1 -- Jmol 11.1.13  2007-02-14 15:54;
 1 H H1_#1 2.9400268 2.3187106 -0.35901633 ;
 2 N N2_#2 -1.4280989 2.2970076 0.9680812 ;
 3 C C3_#3 -0.5195322 0.37288004 -0.24890617 ;
 ...
 24 H H24_#24 0.7507625 -1.5374694 -1.5575587 ;
 end coord set;
 
 
 which allows setting of atom coordinates in bulk. This is necessary, of
 course, because if you move the atoms, we have to reproduce that in the
 script.
 
 So with that, it seemed simple enough (about 10 lines of code) to create:
 
   write coords
 
 which writes the same SPT script as
 
   write state
 
 except it also includes coordinate positions.
 
 SO, having done that, it seemed ridiculous if Jmol could write
 coordinates but not read what it had written, so I added a tiny
 JmolDataReader to read those files.
 
 I really don't know if that is of any particular use. But it was simple
 enough to do.
 
 But more useful, probably, would be the ability to write the coordinates
 in a more standard format, and if people feel strongly that we should
 NOT be able to read these script files this way, I would be happy to
 remove that capability.
 
 Comments? Suggestions for perhaps a SIMPLE general format for writing
 coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited,
 but with bonds), PDB? (unlimited, but rather involved).
 
 Alternatively, should Jmol have a new native format that includes the
 state?
 
 I don't want to make a big deal about this; just wondering.
 
 And, yes, I know -- the next thing needed is rotateSelected. I'm
 working on that. When that is in, we can start having quite some fun
 with loading two files, inverting one, moving it above the other,
 rotating it independently, etc. I think there might be some nice
 applications that would use this capability.
 
 
 Bob
 
 
 
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Re: [Jmol-users] advice needed

[Dean Johnston]

WOW!  This is what I needed two months ago.  You just made about half of my
Javascript code unnecessary, but it's so much easier and cleaner to do it
within Jmol.

 OK, I've got rotation, translation, and inversion of selected atoms
 going now. It can all be scripted using
 
 rotateSelected
 translateSelected
 invertSelected
 
 The question is: How to specify this with the mouse? Right now I've set
 it up (11.1.13) so that if you
 
 set allowRotateSelected
Should you do something like:

set altMouseMode ( rotateSelected | translateSelected | invertSelected )
???

It would be cool to be able to control inversion with the mouse..  (I really
like the rotateSelected with the mouse)

Another idea.  Can you RESTRICT the rotateSelected to be only around an
arbitrary axis?

 Here's a quiz for you. What does the following script do?
  Ummm, synchronized spinners?  Oddly enough, one molecule disappeared after
a minute or two.

 great -- you can use the Miller indices and select symmetry operation sets:
 select symop=1555
 invertselected HKL {1/2 1/2 0}
  Yeah, it's been a while since I've used Miller indices - ok, that will be
MUCH simpler.

 Let's see.. What's an improper rotation again? Oh, sure, that's trivial --
Yes, just roto-reflection.  Trivial.

Dean



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Re: [Jmol-users] Jmol and Moodle

[Dean Johnston]

Jeff,

  I'm interested in getting our college to use Moodle as well, so I'll be
interested to see whether this can be resolved.

  I checked on my MacBook (logging in as guest on a site in the UK -
http://moodle.yeovil.ac.uk/course/view.php?id=63) and was able to reproduce
what you observed.  Jmol loaded the molecules just fine on Safari as well as
IE and Firefox under WinXP (Parallels), but failed for Firefox on the OS X.
They are using Jmol 11.0.RC4, so I don't think it is a Jmol version issue.

  For those of you with more knowledge of the internal workings of Jmol, the
Java console gives the following:

FileManager opening http://moodle.yeovil.ac.uk/file.php/63/caffeine.xyz
error opening http://moodle.yeovil.ac.uk/file.php/63/caffeine.xyz
unrecognized file format for file
http://moodle.yeovil.ac.uk/file.php/63/caffeine.xyz

  I would guess it's a Moodle configuration issue.  Concerning the Java
embedding plug-in, it should be included as part of all recent versions of
Firefox for OS X.

  FYI, if you do change Jmol versions and you want to use Firefox on OS X,
make sure to get a recent version (11.1.10 or later) that fixes a slightly
annoying jumpiness when rotating or zooming molecules.

Dean Johnston
Department of Chemistry and Biochemistry
Otterbein College


On 2/13/07 2:19 PM, Jeff Hansen [EMAIL PROTECTED] wrote:

 My university is currently trying Moodle as an alternative to Blackboard for a
 Course Management System.  One of the things I like about Moodle is that it
 supports Jmol.  However, we have had some problems so far.  I have put a
 couple of Jmol pages on my Moodle site.  I am able to view the molecules just
 fine in Safari but not in Firefox (Mac OS X 10.4.8).  In Firefox, it loads the
 applet just fine but fails to load the molecule.  I get a black box which,
 when I control click, gives the pop-up menu which indicates no atoms are
 loaded.  We are using Jmol 10.2.  I have asked them to switch to 11.0, but it
 hasn't happened yet.  If anyone has any suggestions about what is going wrong
 that I could forward to our Moodle site administrator I would really
 appreciate it.  I haven't yet had the chance to test on any other systems so I
 don't know how it behave there.
 
 Thanks.
 
 
  
 *
 Jeff Hansen
 Department of Chemistry
 DePauw University
 Greencastle, IN 46135
 [EMAIL PROTECTED]
 *



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[Jmol-users] Selecting range of models

[Dean Johnston]

I have a file with about 15 models in it and I want to select all but the
first model.  I've figured out a way to do this (after some trial and
error), but I'm not sure it makes sense to me.  I can just say:

SELECT not */1or   SELECT not 1.1

and I get what I want (there is an inferred ALL in there).  My first thought
was to say SELECT * not 1.1 or SELECT all not 1.1, but they gave errors.  I
guess I just want to be more explicit about the sets that I am combining
using the NOT.  Does this make sense?  Perhaps there should be a select
RANGE option similar to the FRAME command.

  On a related note, the SELECT documentation (
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples/select.htm)
appears to have a Javascript error in it (Error: jmolSetDocument is not
defined, Source File:
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples/examples.js
Line: 88) and doesn't load for me.

Dean Johnston



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[Jmol-users] Jmol Wiki not working

[Dean Johnston]

When I try to get to the Jmol Wiki, I get a page that is definitely NOT the
Wiki.  Is this just a problem with SourceForge?  www.jmol.org gives an error
as well.

Dean Johnston



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Re: [Jmol-users] Jmol Wiki not working

[Dean Johnston]

This is what I see:

The first link (wiki.jmol.org) loads a page that is basically an
advertisement for GoDaddy.  Not the Jmol wiki.

The second link (www.jmol.org/wiki) gives a 404 error.

Dean


On 2/13/07 4:53 PM, Nicolas Vervelle [EMAIL PROTECTED] wrote:

 Dean Johnston wrote:
 When I try to get to the Jmol Wiki, I get a page that is definitely NOT the
 Wiki.  Is this just a problem with SourceForge?  www.jmol.org gives an error
 as well.
 
 Dean Johnston
   
 (My mails are rejected by sourceforge, but you can continue the
 discussion on Jmol-users list if you want)
 
 The Jmol Wiki is currently working, I think only sourceforge
 (www.jmol.org) is having troubles.
 How are accessing the wiki ?
 http://wiki.jmol.org/ should work
 http://www.jmol.org/wiki shouldn't work
 
 Nico



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Re: [Jmol-users] Selecting range of models

[Dean Johnston]

Yes, of course it makes sense now.  I'm typically using NOT in the context
of database searching where it is much less mathematically precise.  Thanks
for the clarification.

Dean


On 2/13/07 6:18 PM, Bob Hanson [EMAIL PROTECTED] wrote:

 
 Dean Johnston wrote:
 
 I have a file with about 15 models in it and I want to select all but the
 first model.  I've figured out a way to do this (after some trial and
 error), but I'm not sure it makes sense to me.  I can just say:
 
 SELECT not */1or   SELECT not 1.1
 
 and I get what I want (there is an inferred ALL in there).  My first thought
 was to say SELECT * not 1.1 or SELECT all not 1.1, but they gave errors.  I
 guess I just want to be more explicit about the sets that I am combining
 using the NOT.  Does this make sense?  Perhaps there should be a select
 RANGE option similar to the FRAME command.
 
  
 
 not is a unary operator - that is, it operates on the next item but
 doesn't connect two. So
 
 select not */1
 
 makes sense. The not */1 is always done first.
 
 select * and not */1
 
 also makes sense, but is unnecessary, since ALL and does nothing.
 
 You can say
 
 frames all;
 display */1 and not */1.3;
 
 to display all the models of file 1 except model 1.3
 
 Bob



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[Jmol-users] DATA command broken in 11.1.12?

[Dean Johnston]

The DATA command has stopped working for me somewhere between 11.1.8 and
11.1.12.  Issuing the simple command:

data model example|2|testing|C 1 1 1|O 2 2 2|end model example;show data

hangs the applet (says script pending) and starts chewing up processor
cycles.

Observed on OS X and WinXP.

Dean



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[Jmol-users] Coloring objects translucent broken in 11.1.9?

[Dean Johnston]

I just switched to 11.1.9 and Jmol no longer colors my objects (planes,
isosufaces, polyhedra) translucent.  I can still color atoms and bonds
translucent.

Dean Johnston



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[Jmol-users] Appending and/or selectively deleting models

[Dean Johnston]

I don't know if there is an existing way to do this, but it seems like it
might be generally useful.

I'd like to take a model and append (instead of completely replace) a second
model using the DATA command.  Similarly, I'd like to be able to selectively
DELETE models.  Does anybody else think this might be useful?

Dean Johnston



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Re: [Jmol-users] Drawing small spheres using the isosurface command

[Dean Johnston]

Angel,

  Thanks - the resolution parameter was the first thing I tried.  It was
late and I guess I was entering the parameters in the wrong order.

Dean


On 1/26/07 5:55 AM, Angel Herraez [EMAIL PROTECTED] wrote:

 Hi Dean 
 
 There is a resolution value for isosurfaces, so I guess your problem
 may be to be drawing below that.
 
 From Jmol interactive scripting documentation:
 RESOLUTION x.x 
 Sets the resolution of a constructed isosurface three-dimensional
 grid of voxels, in points per Angstrom. Does not apply to CUBE or
 JVXL files, which have a resolution defined by internal file
 parameters.
 
 The resolution parameter goes before the sphere; raise it until
 you get no holes:
 
 isoSurface resolution 16 sphere 0.3
 
 isoSurface resolution 28 sphere 0.2
 
 isoSurface resolution 50 sphere 0.1
 
 --tested in 11.0.RC4--



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[Jmol-users] Drawing small spheres using the isosurface command

[Dean Johnston]

Has anybody played around with drawing spheres using the isosurface command?
It works fine for me until I try and draw a sphere with a radius less than
about 0.5 Angstroms, at which point holes appear in the sides.

Example command: isosurface myCenter sphere 0.4

Perhaps Jmol was not designed to draw small isosurface spheres, but I want
to draw psuedo-atoms that are about the same size as the atoms in a
ball-and-stick representation.

Dean Johnston



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[Jmol-users] Translucent objects are not visible through other translucent objects

[Dean Johnston]

I know this is probably too much to ask, but is there any way to make
translucent objects show up through other translucent objects?  For example,
if I draw a translucent plane, any translucent atoms that move behind the
plane just disappear as if the plane is opaque.  It sort of destroys the
illusion of translucency.  I have a simple (very artificial) example page at
http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/trans_test.html.  In that
example, the oxygen and the plane are translucent and the hydrogens are
opaque -- but you can't see the oxygen through the translucent plane.

Dean Johnston



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[Jmol-users] Selecting one atom in one model/frame - should this work?

[Dean Johnston]

I need to be able to select one atom in one model in a multi-model file.  My
first attempt was to do the following:

  select (atomno=1)/1

but this gives script compiler ERROR: end of expression expected

I know that I can just say:

  select (atomno=1)  (model=1)

but it seems like the first method should work as well...  Am I missing
something?

Dean Johnston




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