>>
>
> I suspect this would be easier for users and could likely be made more
> secure. However, I have no idea how this would be implemented. The
> mediawiki language seems to aim to remove as much direct html use as
> possible.
>>>
Our students use Jmol Mediawiki extensively. We have come up aga
A simple Alchemy reader is now part of Jmol.
See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/p
Dear Bob,
Date: Tue, 9 Dec 2008 18:20:58 -0600
> From: "Robert Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
>schematic base-pair geometry
> To: jmol-users@lists.sourceforge.net
> Message-ID:
><[EMAIL PROTECTED]>
> Content-Type:
I'll set it up tonight
On Dec 9, 2008, at 7:21 PM, "Xiang-Jun Lu" <[EMAIL PROTECTED]> wrote:
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
From: "Robert Hanson" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Support of 'alchemy' format for r
You can also embed these javascript calls into the pdb file itself,
if it has an embedded Jmol script into it.
Paul
Le 9 déc. 08 à 14:41, Angel Herraez a écrit :
> El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió:
>> For example, I think you can stillrun Javascriptwithscripts
>> calling oth
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
> From: "Robert Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
>schematic base-pair geometry
> To: jmol-users@lists.sourceforge.net
> Messa
On Tue, Dec 09, 2008 at 02:03:17PM +0100, Nicolas Vervelle wrote:
> Hi,
>
>
> On Tue, Dec 9, 2008 at 1:21 PM, Angel Herraez <[EMAIL PROTECTED]> wrote:
>
> > I'd like to keep this discussion going, so here is a little bit more,
> > picking up on the possibilities to have Jmol supported in Wikiped
On Tue, Dec 09, 2008 at 01:21:01PM +0100, Angel Herraez wrote:
> I'd like to keep this discussion going, so here is a little bit more,
> picking up on the possibilities to have Jmol supported in Wikipedia
> and other Wikis:
[Nico's message snipped]
> And on 1 Dec 2008 9:49, Brian Salter-Duke w
On Tue, Dec 9, 2008 at 10:02 AM, Xiang-Jun Lu <[EMAIL PROTECTED]> wrote:
>
> As far as Jmol's support for alchemy is concerned, I converted a sample PDB
> file to alchemy using 'openbabel' and Jmol can read it without a problem.
Can you send me that converted file? I'd like to see what Jmol is doi
make that
then just
> drawbox("box1", {-2.2500 5. 0.2500},{-2.2500 -5. 0.2500}
> ,{-2.2500 -5. -0.2500} ,\
> {-2.2500 5. -0.2500},{2.2500 5. 0.2500},{2.2500
> -5. 0.2500},\
> {2.2500 -5. -0.2500},{2.2500 5. -0.2500})
>
> for each box. It se
Before I write this reader, can I ask if it's possible you could use
another format?
Do you have all these files already made, so you are eager to use them
exactly, or do you have a program that produces them?
Because if it's a program that produces them, I suggest doing a little
modification to
On 9 Dec 2008 at 17:14, Nicolas Vervelle wrote:
> I am rather thinking as Rolf does, that to convince Wikipedia people it would
> be better to really
> deactivate Javascript in Jmol itself (would it be possible to pass an option
> to Jmol applet
> whenstarting it ?), rather than trying to bloc
On Mon, Dec 8, 2008 at 3:33 PM, Xavier Prat-Resina <[EMAIL PROTECTED]> wrote:
> OpenBabel reads the Alchemy format
>
> http://openbabel.org/wiki/Alchemy
>
> which makes me wonder if Jmol could use the versatility of Open Babel and
> avoid writing new code.
It's very easy to write a file reader --
I think you just say
{within(3.0, [lig])}.temperature= 3.0
or
{within(3.0, [lig])}.partialCharge = 0.3
On Mon, Dec 8, 2008 at 7:45 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote:
> Hi Bob,
>
> Is there a script command I can use to add values for the temperature
> property of the selected ato
I think this is all fixed now. The sequence of execution is:
file load
-J (Jmol script as argument)
-s (script file name as argument)
-j (Jmol script as argument)
-x (exit)
The -n switch (no display) adds an implicit -x, and it is executed
only after the final script is run. Basically what the -x
On Tue, Dec 9, 2008 at 2:41 PM, Angel Herraez <[EMAIL PROTECTED]> wrote:
> El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió:
> > For example, I think you can stillrun Javascriptwithscripts
> > calling other scripts:
> > * Create a wiki page with contents corresponding to a Jmol script with
>
Dear Prof. Robert,
Thank you very much for that.
I have something maybe interesting for you. I read from Rich's
blog(http://depth-first.com/articles/2008/07/15/javascript-for-cheminformatics)
that you're interested in AJAX technology used in chemistry.
So I'm thinking, if molecule editor is able
> OpenBabel reads the Alchemy format
>
> http://openbabel.org/wiki/Alchemy
>
> which makes me wonder if Jmol could use the versatility of Open Babel and
> avoid writing new code.
>
> Xavier
>
I have been using 'openbabel' for a long while, and know that it supports
alchemy format. However, it can'
[EMAIL PROTECTED] wrote:
> Quoting Robert Hanson <[EMAIL PROTECTED]>:
>
>> Rolf, will this cause any real problem? You just need to add load
>> \"...\"; at the beginning of your -j script.
>>
>> the command line parser -- presumably standard Java -- does not accept
>> quoted strings as values for
Duan Lian,
Your request for a better way to pass an image to an output stream
gave me an idea. I have now checked in two new methods for Jmol that
can be accessed by an embedding application or a browser using the
signed applet:
Object nullOrBytesOrStringOrErrorMsg =
jmolViewer.getImageAs(ty
Arjan,
I have used Eric Martz' MORPH2 to calculate intermediate co-ordinates from a
beginning and a final PDB file. MORPH2 is a part of pdbtools, available from:
http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz
Go all the way to the bootom of the page to download pdbtools.
I've used Chem3D and Spartan to make movies. I liked Chem3D better because
Spartan would sometimes change the xyz coordinates to yzx when I changed from
one structure to the next.
-Jennifer
--
Message: 1
Date: Mon, 8 Dec 2
Angel Herraez wrote:
> El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió:
>> For example, I think you can stillrun Javascriptwithscripts
>> calling other scripts:
>> * Create a wiki page with contents corresponding to a Jmol script with
>> Javascript in it.
>> * Add a tag in a page
El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió:
> For example, I think you can stillrun Javascriptwithscripts
> calling other scripts:
> * Create a wiki page with contents corresponding to a Jmol script with
> Javascript in it.
> * Add a tag in a page with a script calling the ot
Hi,
On Tue, Dec 9, 2008 at 1:21 PM, Angel Herraez <[EMAIL PROTECTED]> wrote:
> I'd like to keep this discussion going, so here is a little bit more,
> picking up on the possibilities to have Jmol supported in Wikipedia
> and other Wikis:
>
>
> On 30 Nov 2008 22:53, Nicolas Vervelle wrote:
> >
>
I'd like to keep this discussion going, so here is a little bit more,
picking up on the possibilities to have Jmol supported in Wikipedia
and other Wikis:
On 30 Nov 2008 22:53, Nicolas Vervelle wrote:
>
> On the matter of security issues, there are at least 2 things to do :
> * Being able to
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