Begin forwarded message:
From: Otis Rothenberger osrot...@chemagic.com
Subject: Re: [Jmol-users] Jmol for iPads?
Date: 29 March 2012 15:44:43 GMT+01:00
To: jmol-users@lists.sourceforge.net
Reply-To: jmol-users@lists.sourceforge.net
I'm saddened by the fact that for the foreseeable
On 2 Mar 2012, at 16:54, Robert Hanson wrote:
Well, then I propose /*file*/ within a script is adapted by MediaWiki
to change that to a proper file name.
On Fri, Mar 2, 2012 at 9:51 AM, Nicolas Vervelle nverve...@gmail.comwrote:
an alternative which by-passes the file path naming
On 2 Mar 2012, at 13:23, Angel Herráez wrote:
I agree with Nico. The location of uploades files in MW is uncertain.
The .jmol file format is in my opinion the way out of this problem:
upload a single file with everything included.
A single file as a zip (the same way that jar files are
On 1 Mar 2012, at 14:24, Jaime Prilusky wrote:
On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote:
The MediaWiki extension has the following form
Overall, this amounts to
load isosurface.xyz;isosurface color orange purple isosurface.jvxl
translucent;
Yes, putting the full filename path
On 1 Mar 2012, at 15:09, Jaime Prilusky wrote:
On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote:
If you have ideas of what syntax should be used in the extension to make
using it simple, don't hesitate.
If you keep the isosurface file together with the model file, then a simple
On 21 Jan 2012, at 12:59, Robert Hanson wrote:
Looks totally doable. What we need to follow up on this are:
a) A reader/viewer we can use for testing.
b) A bunch of examples. (OK, I have those from
The recent announcement by Apple of an interactive e-book authoring environment
(iBooks Author) has an example of a molecule captured using the Collada format
http://www.khronos.org/collada/
Can I ask if it might be possible for Jmol to emit this format (or should we go
the iBabel route?).
On 5 Dec 2011, at 22:06, Paul Pillot wrote:
ChemDoodle is proprietary, but Chemdoodle web components (that's what Bob
referred to) is open source (GPL)
It uses javascript and doesn't need Jmol on the server side. You can feed the
script with a PDB file and it will eventually render it in
On 27 Oct 2011, at 06:12, Robert Hanson wrote:
Taking the lead from Otis Rothenberger, I have added the following command
to Jmol:
show NMR
Could also add the simulator as an alternative to the predictor
http://www.nmrdb.org/simulator
(By the way, Wow! Do I LOVE this little dual-core Galaxy. I am very happy I
didn't jump for an iPad now; this is a real computer, not just a large
iPhone!)
I'm starting to catch on to the tablet idea,
Bob,
If you have any spare time (!), I would be interested in how much having the
Thaks to Pshemak Maslak for a hint. As usual, simply asking a question
focuses wonderfully. So to summarise:
If generating an MO from a cube, then something along the lines of
isosurface MO cutoff @x sign blue red HHa_mo15.cub;
will generate jvxl with these colours. The simplest way
To avoid confusion regarding my last post, I would elaborate that in
isosurface MO cutoff @x sign blue red HHa_mo15.cub;
@x is a variable, and would normally be given the explicit value eg 0.02
As for the two lines in the jvxl
colorNegative=[x00]
colorPositive=[xffa500]
I now
I am loading two MO surfaces thus
load HHa_mo15.xyz;isosurface HHa_mo15.jvxl translucent;isosurface append
HHa_mo17.jvxl translucent;
I want to show the overlap between two MOs. It is of course a 50%
probability that the phases will match to show the effect I want. Can anyone
offer a
The issue I reported is now solved for MediaWiki 1.17 (thanks Nico!). We
are still testing, but if anyone is desparate, contact me (or Nico).
On 14 Sep 2011, at 09:11, Egon Willighagen wrote:
On Wed, Sep 14, 2011 at 10:09 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On 8 Jun 2011, at 14:50, Robert Hanson wrote:
This is better: http://www.youtube.com/watch?v=AilBZeeeETk
Bob, could you invert the rainbow? Its just that Julia uses blue =
attractive and you are using red = attractive?
On 8 Jun 2011, at 15:09, Robert Hanson wrote:
I'm not going to remake the movie -- these aren't her colors anyway,
because
this would all be green. I just left the colors there because it was
more
interesting.
I just dont want multiple colour schemes out there. Julia uses +5 to
-5
On 8 Jun 2011, at 15:09, Robert Hanson wrote:
I'm not going to remake the movie -- these aren't her colors anyway,
because
this would all be green. I just left the colors there because it was
more
interesting.
Bob,
Between colorscheme translucent bgyorand FULLYLIT
On 18 Apr 2011, at 01:23, tvrb wrote:
wagquack wrote:
However I did not find the option described in the standalone
application?
Could somebody please help me and tell me if this is possible ?
wagquack, it looks like your article shows exactly how to get
stereographic
3d. Open a
On 23 Feb 2011, at 01:33, Robert Hanson wrote:
Well, at least I think so
http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol
Please let me know if that does not work for you.
Bob,
The issue of whether the path passes through a boat
I note on this site the intention to fully match the functionality of Jmol
using WebGL technologies
http://www.ichemlabs.com/1201
and you can try http://www.molecularmodelingbasics.blogspot.com/ using a
WebGL supported browser (I use WebKit version of Safari). No doubt Apple will
On 7 Feb 2011, at 14:20, Robert Hanson wrote:
Jmol users,
Here's a link to the Prezi presentation I'm planning to make at the
International Council for Scientific and Technical Information
Winter Workshop tomorrow in Redmond, Washington. The focus of the
workshop is on Multimedia and
Hi everyone,
I am trying to enhance the http://wiki.jmol.org/index.php/MediaWikiJmol
MediaWiki Extension to automatically display with some molecule files in
Wikipedia.
I want to start with file formats recognized by Jmol that are using XML
syntax, because it seems easier to
Can someone
Looks more promising
http://www.appleinsider.com/articles/10/11/12/oracle_and_apple_announce_openjdk_for_java_on_mac_os_x.html
--
Professor Henry S Rzepa.
+44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/ /rzepa/blog
Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
At 11:24 +0100 22/10/10, Egon Willighagen wrote:
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
fun!
On Sat, Jul 24, 2010 at 3:10 PM, Thomas Stout
mailto:thomasjst...@gmail.comthomasjst...@gmail.com wrote:
Just an FYI... I ran across this today:
http://www.molsoft.com/ipad.htmlhttp://www.molsoft.com/ipad.html
I note with interest that whilst the iPad can receive (by email or iTunes)
I gave something along the following a try using 12.0.RC27_dev (signed applet)
isosurface laplacian cutoff 0.2 sign C5_lap.cube;color isosurface
translucent;write C5.idtf;
and it produced a .idtf and a .idtf.tex file of non zero length. But they were
very small (4k/8K) and looked empty to
Can anyone cast light on the issue described at
http://www.ch.ic.ac.uk/rzepa/blog/?p=1930 ?
--
+44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/
Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
(Voracious anti-spam filter in operation for received email.
If expected
If you have not seen it, take a look at http://touchpress.com/
The e-book contains rotating 3D models, and even Stereo (with appropriate
glasses).
At the risk of sounding like a broken record (what is the modern metaphor for
this?), I would like to put soundings out again for eg
I would like to place a label on an atom which contains eg a greek letter.
Clearly, since the normal way of declaring an entity, ie delta; is not
possible, since ; is a reserved character in scripts, I tried eg delta%3B
(%3B is the escape code for ;. But that does not work either.
I would therefore advocate making this option as easy as possible to use
within Jmol. In my view, interactive 3D pdf figures should really be the rule
rather than the exception in scientific publishing, and Jmol could lead the
way.
Publishers are likely to love interactive PDF, since it is
It's not clear to me if many publishers yet have a coherent strategy
regarding interactive figures.
I have had around five publishers accept the concept of Jmol-enhanced
interactive figures (the latest being Science). However, it has to be said that
the first publisher to do so (about 4 years
Fuji have recently introduced a 3D camera, and with it a print service onto
so-called lenticular prints. The format they use for 3D is MPO+JPEG
http://www.fujifilm.com/products/3d/camera/finepix_real3dw1/specifications/index.html
Hi,
There are 2 pages on the wiki for this :
http://wiki.jmol.org/index.php?title=Jmol_in_Wikis_and_Blogshttp://wiki.jmol.org/index.php?title=Jmol_in_Wikis_and_Blogs
http://wiki.jmol.org/index.php?title=CMS_Using_Jmolhttp://wiki.jmol.org/index.php?title=CMS_Using_Jmol
You can expand it with your
Hi all,
is Jmol still able to save the content? For example as CML or perhaps
MDL molfile or XYZ?
As it happens, Bob and I have been having a discussion about eg saving XYZ
(with vibrational vectors). Bob's documentation does describe the process,
although of course one has to use the
On Fri, Oct 30, 2009 at 3:03 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
As it happens, Bob and I have been having a discussion about eg saving XYZ
(with
vibrational vectors). Bob's documentation does describe the process,
although of course
one has to use the signed applet to use
There do have some iPhone/iPod touch app for 3D molecule viewing. Here
is one http://www.sunsetlakesoftware.com/molecules .
I think there is a connection of sorts between the above app and Jmol. The
app I think relies on the original Roger Sayle Rasmol opensource codes; I
presume it was
With HTML5 and its multimedia components being finalised (the W3C
specification is being edited by one person from Apple, and another from
Google!),
http://homepage.mac.com/swain/Macinchem/Reviews/Chemdoodle/chemdoodle_web_components.htm
makes for an interesting comparison with Jmol. It
At 16:30 +0100 25/8/09, N David Brown wrote:
Henry,
Speaking from a programmer's perspective, I find your comparison
premature. It's the equivalent of saying that the HTML 5 canvas tag
will replace Flash - true, it's possible this could happen one day.
However, given that (i) HTML 5 is not yet
Quick follow up to http://www.ch.ic.ac.uk/local/organic/pericyclic/2HK4.html
Kinemage (which is more veritable than Jmol), also fails to close the cycle
on cyclic DNA, so I presume that Jmol is merely following the convention in
this regard in how it also does this.
I guess this is a bit
Brian,
We are currently running courses with no issue using the old
implementation
http://www.ch.ic.ac.uk/wiki/
(which has proved VERY robust. We often have classes of 50 students
all hammering pages with 10 or more embedded Jmols, with no issues).
but have also been struggling to
On 29 Nov 2008, at 01:41, Brian Salter-Duke wrote:
The question of having Jmol used on wikipedia has again been raised on
the commons email list. On contributor to the discussion says that the
jmol mediawiki extension now only works with an older version of
mediawiki. Certainly my examples
I have gotten the Jmol Mediawiki to display a variety of more
interesting modes:
https://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol
(although I dont think it can do everything a conventionally invoked
applet can).
-
On 29 Nov 2008, at 18:43, Angel Herráez wrote:
Henry, I'm glad that you found the cure for your problem, and to
have been a catalyst in that
cure :)
On 29 Nov 2008 at 14:53, Rzepa, Henry wrote:
In the distribution
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki
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
(http://www.geowall.orgwww.geowall.org), it's a low-cost stereo projection
system. You setup a computer with a dual-head video card, two projectors
with polarizing
On Wed, Oct 8, 2008 at 8:01 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Excellent! Say, did you know we came close to 10,000 downloads last month?
Oh, and ranked 62 overall on SourceForge (today)... this means Jmol
has en enormous impact!
Here's of the last few months:
On 9 Oct 2008 at 9:01, Rzepa, Henry wrote:
It would be interesting to identify all the STM journals that deploy it in
some manner or other.
Sorry, what is STM?
STM = Scientific, Technical and Medical
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf
Amazing!
Thanks for pointing this out, Wayne. I have missed the last two email
ToC for TIBS, which I regularly review.
Movement of the model is very smooth. The quality of the renderings
is not so good -- must be related to file size, since PyMol can have
a very good quality.
I too am
Just to save anyone else the pain of getting Jmol working with Google's new
browser Chrome http://www.google.com/chrome/http://www.google.com/chrome/
You need a pre-release version of Java
http://java.sun.com/javase/downloads/ea.jsp then it works (so far).
Apparently the reason is performance
Just to save anyone else the pain of getting Jmol working with Google's new
browser Chrome http://www.google.com/chrome/http://www.google.com/chrome/
You need a pre-release version of Java
http://java.sun.com/javase/downloads/ea.jsp then it works (so far).
Also highlighted is the capability
See http://pubs.acs.org/4librarians/livewire/2008/9.3/index.html
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED]
(iChat)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7
2AZ, UK.
(Voracious anti-spam filter in operation
For the Jmol application, I have some doubts because the application will
probably have to be distributed through App Store.
If I understand correctly, there's an annual fee for distributing an
application (99$ ?)
Nico
Only if one charges for the product? But understand that the Java
will
Along with
http://www.regdeveloper.co.uk/2008/03/08/jvm_for_the_iphone/
and
http://developer.apple.com/iphone/
can we expect Jmol to appear there in the near future?
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED]
(iChat)
Higly recommended, in the current issue of Nature
(http://www.nature.com/nature/journal/v451/n7179/full/451648a.html ):
Peter Murray-Rust's ambitious and inspiring vision of the future of
free exchange of, and wide access to scientific information,
particularly in chemistry. The emerging world of
Dear Jmol users,
I would like to draw to your attention a new site I have developed using Jmol
(with much help from many of you, especially Bob) to depict
interactive 3D animations for some of the most important organic reactions
covered during an undergraduate degree with supporting information
Steve Jobs at the WWDC:
Jobs also confirmed that iPhone won't support Java. [It's] not worth
building in, he said. Nobody uses Java anymore. It's this big
heavyweight ball and chain.
Whilst this might not seem to matter just for the iPhone (although it
would have been nice to display Jmol in
Mmmm...
So nobody is using Java? Where does he live?
And if he doesn't say what's the alternative, is this assertion trustable?
I understood that iPhone uses plain MacOSX, so how is Java prevented
from working? Do they block installation? What happens with other plugins,
like Flash? Can't the
Some comments on these bits:
I have been asked questions
such as what is the lifetime of a WEO, and what happens
in eg 10 years time when the Java virtual engine is no longer
installed/supported on the majority of Web browsers.
Jmol is opensource! There is absolutely no reason not to
Fast and furious! 11.1.14 is ready. Forget 11.1.13 -- this is better. :)
3.6 Mbyte for the consolidated jar file? It used to be around 1.1?
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax);
[EMAIL PROTECTED] (iChat)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry,
Fast and furious! 11.1.14 is ready. Forget 11.1.13 -- this is better. :)
Its early in the morning, and I clearly have not woken up yet.
Scrub that last post;
I was looking at the application, not the applet!
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax);
[EMAIL
OK, Jmol 11.1.11 will have something for Henry Rzepa:
set echo top left
echo %{_memory}
You will see two numbers show up in that echo, and they will update
automatically as you rotate the model and such.
10.3/15.4
means Jmol is using 10.3 Mb of memory and has been allocated 15.4 Mb.
These
Dear Colleagues,
Eric Martz and I are happy to announce version 2 of the BioMolecular Explorer
3D web site, (designed to supplement a secondary school biology curriculum)
which uses Jmol in place of Chime to present macromolecular structures and
tutorials. This simplifies the process of using
Nico,
In the mediawiki invocation of Jmol, how might one address
different instances of a jmol. Might it be eg
jmol name=first or jmol id=first?
Would either of these be supported by your code?
Much of http://wiki.jmol.org/index.php/MediaWiki#Simple_usage
seems to assume only one jmol per
Whilst perhaps not so polished as Sculpt , I would note projects such as
Ghemical, http://www.uku.fi/~thassine/projects/ghemical/
an opensource project for energy minimisation, with a graphical
front end (http://www.uiowa.edu/~ghemical/
I gather a project to implement a universal-force-field
Could someone please explain how to achieve the following code result
uploadedFileContentsEthanol.xyz/uploadedFileContents
When I try to upload a file, mediawiki tells me its not a recognised
image file, and refuses it. I guess a setting has to be tweaked somewhere
(perhaps even setting a
Am Dienstag, den 04.04.2006, 10:44 +0200 schrieb
[EMAIL PROTECTED]:
Hi everyone,
The Jmol Wiki is now using a totally new version under MediaWiki instead of
MoinMoin Wiki.
The URL is still the same: http://wiki.jmol.org/
It seems, that everyone is allowed to change content. I highly
Could I ask the list to test the following
http://pubs.acs.org/subscribe/journals/chreay/suppinfo/cr030092l/Figure4/index.html
When I tested it locally, molecules ALWAYS appear on the page. When the ACS
mounted it, molecules always appeared when they test it. But when I
and colleagues here
Same here.
BTW, great to see Jmol in action like this! Thanx.
Egon
As I have mentioned in the past, testimonials to the use of Jmol
in eg Journal pages could perhaps be collected by some volunteer on the
sf pages.I have about 10 examples sprinkled around various journals,
including
De: Rzepa, Henry [EMAIL PROTECTED]
As I have mentioned in the past, testimonials to the use of Jmol
in eg Journal pages could perhaps be collected by some volunteer on the
sf pages.I have about 10 examples sprinkled around various journals,
including my favorite, http://www.ch.ic.ac.uk
If noone has such a program, then *maybe* I'll do it and include it in the
Jmol distribution. Tell me some reasonable defaults for:
1. upper limit
2. lower limit
3. digits of precision
Gosh, we did this about 12 years ago, and we worked this all out then,
but I would have to look at it
Hi all,
I can't remember this link being posted to this list, but it's worth checking
out!
http://chemie.skku.ac.kr/~wkpark/demos/demo/sample.html
Thanx Park!
Am I correct in inferring this originates from
http://archive.ncsa.uiuc.edu/Edu/ChemViz/documentation/waltzdocs.html ?
and a
I am sorry I am rather late for this thread. Wanted to add that
Marion Cass will be presenting Jmol via our pseudorotation
page; http://www.ch.ic.ac.uk/rzepa/bpr/
This article is one of three that have been submitted to J Chem Ed
extolling the virtues of Jmol. An earlier one on symmetry
I am not aware of pmesh outputs; those that I have seen are either 3dmf
(which is a more abstract language, containing objects other than planes,
and hence capable of interfacing with eg openGL for performance)
or the Gaussian cube format (which needs isosurface rendering to turn into
a
When the fancy takes us, we occasionally sit down and write a short article
for publication (mostly of pedagogic nature) describing some use of Jmol.
Other than simply citing the
sf Web site, its always nice to put in a proper full citation. Information on
how this
might be done happens to
Also http://www.ch.ic.ac.uk/chemime/tests/object/
(this being a test of the object tag, which fails miserably in 10.3!)
Netscape 7.1/Windows XP: I do see a crude model, which I can manipulate with
the mouse. So I guess that object is working. But the Load links don't do
anything as far as I
Henry et al,
I'd be delighted to test any Jmol based pages with OS X 10.4.
Please let me have the URLs and details of the OS/browser combination that
produces ideal results.
To date I can say that things are generally better with Safari than under
Panther. All the Jmol home site is fine.
I'm 100% with Miguel when he says that if you can get your clients to upgrade
to Sun 1.4 or 1.5, please do so! That's the best solution!
Well, Apple have quite confused this aspect. They offer both 1.3 AND 1.4 (but
not
yet 1.5, which will come with Tiger). For reasons totally beyond
applet height=12
archive=JmolApplet.jar,gnujaxp.jar width=12
code=JmolAppletControl mayscript=true
param name=target value=Int1 /
param name=type value=chimeToggle /
param name=script etc
Don't know why
I have tracked it down to the following. If eg a .mol or .xyz file is
loaded, it has no problems on either
Mac or Windows. But if a CML file is loaded (as here),
on Windows one appears to get
the following errors. Is this a SAX parser error?
I thought this was built into Jmol (V
There is no XML parser built into the Java 1.1 libraries. Therefore, in
order to support CML on IE Windows you must provide an additional .jar
file: gnujaxp.jar
You are writing your own [applet] tags. One of the attributes is
archive='JmolApplet.jar'
change this to be
But except for the missing gnujaxp.jar (which I actually locally added in the
Jmol.jar), we also had problems with testing for the availability of JAXP...
which is not, but the exception thrown were not catched...
InstantiationException and ClassNotFoundException...
This is deja vu all over
But I have just had one OS X user report that his system
behaves like Windows, ie gnujaxp.jar
appears to be missing from his system somehow?
That is because he is running Java 1.3 ... a product which is
approximately 4 years old.
And a version on the Mac which is *not* supported by Jmol.
I like your popup window as an alternative to my suggestion. It is
relatively clear and does not prevent simple pages or people from at
least seeing the molecules.
The javaplugin does not work for me with Firefox 1.0
Fine with Mozilla 1.8a but I agree, its a struggle to keep it working
with
Hi all,
I know this is slightly OT, but I don't know where else I could get the info. Anybody
knows why Safari in OSX 10.3.5 refuses to display greek characters (alpha, beta etc.)
and substitutes with normal characters?
Please reply to the address appended below if you think this is too OT for
More on greek characters (its relevant to Jmol I suppose since all applications
and documents are supposed to become unicode compliant eventually).
The small document http://www.ch.ic.ac.uk/rzepa/greek.html shows two
ways of encoding Greek. The second is document specific, but the first
According to Miguel:
On Wed 8 Sep 2004 Apple posted the final release candidate for Java 1.4.2
Update 2.
Miguel,
Thank you for the early notice on Java 1.4.2 Update 2 for Mac OS X
I installed it and Safari 1.2.3 (v125.9) runs the examples on the Jmol.js
JavaScript Library page without problems.
Excuse if an FAQ (I did not immediately find the answer on the sf site!)
but are there any plans to support pmesh surfaces?
There is an excellent site at
http://www.otterbein.edu/home/fac/dnhjhns/symmetry/details.html
(there may be many others) which does good things with pmesh surfaces!
PS The
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Hash: SHA1
On Wednesday 25 August 2004 12:33, [EMAIL PROTECTED] wrote:
I am not sure I agree with your analysis.
That's good! Apparently you are doing things slightly different... and this
should make it much easier to find the problem...
Could you both
I get the Apple Developer's newsletter. this morning's (or last
night's) edition says something about a java 1.4.2 update. There is a
link which opens a page at Apple dated 5-17-04. Is anyone aware of
this update, what it does, and how it affects jmol? Software update
does not report
On Wed, 14 Apr 2004 10:07:41 +0200 (CEST), Miguel wrote
Rest assured that I am thinking *very* hard about how to make the applet
into an ActiveX control. It could then be embedded into PowerPoint
(or other MSFT applications), and that might just be the *killer
app* for Jmol.
H...not
Thanks Miguel for a truly excellent and clear summary!
Plug-in
---
To understand a plug-in it is helpful to think back to the helper
application. A helper application is not associated with a specific web
page. Rather, it is associated with a specific file type, a specific
mime-type. The web
Found a mechanism to wrap the Jmol.jar into an application on OS X
(thus converting it to jmol.app ) which CAN be treated as a proper
application. Use /Developer/Applications/Java Tools/Jar Bundler
and indicate the main class as org.openscience.jmol.app.Jmol
Whilst I doubt its worth
Rzepa, Henry sent [10.43a gmt 2004 March 18 Thursday] :
Found a mechanism to wrap the Jmol.jar into an application on OS
X (thus converting it to jmol.app ) which CAN be treated as a
proper application. Use /Developer/Applications/Java Tools/Jar
Bundler and indicate the main class
Q: Would it be valuable to have a simpler mechanism to associate the Jmol
application with web browsers as a helper application?
This of course was the MIME handling mechanism, and the reason for
chemical/x-pdb etc MIME types. As far as I can tell, OS X does
not have a clear mechanism for
Q: Would it be valuable to have a simpler mechanism to associate the
Jmol application with web browsers as a helper application?
If the Jmol application can be launched automatically whenever a file
with MOL or PDB extension was loaded by Safari, that would be a big
help.
Henry's message
Egon,
Remind me how one configures the RSS plugin for this version of JMol
(its changed, has it not? )
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
(Voracious anti-spam filter
Perl uses a system call CPAN (Comprehensive Perl Archive Network) to
distribute modules.
become root user and run CPAN to install this module.
su -
perl -MCPAN -e 'install HTML::Parser'
It might ask you a question or two ... just hit [enter] to take the
defaults.
It will then grind and
In the olden days of modem bandwidths, it became common to gzip
molecule coordinate files (compression ratios of 10:1 made this very
worth while, particularly for medium sized molecules). Software
such as Chime would auto-detect this (even though the file name extension
retained the
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