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:
On the
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 jmol tag in a page with a script calling the
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 jmol tag in a page with a
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
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 =
[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 -x flags.
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't read
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
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
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
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 atoms in
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 block
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 doing
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
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 Wikipedia
and
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
Message-ID:
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
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