On Fri, Feb 19, 2010 at 7:48 PM, Otis Rothenberger wrote:
> Bob,
>
> Attempting the latter did raise a question: Can you use variables as
> coordinates in a data statement? I've tried all sorts of x y z variations in
> the "C x y z" component of the data statement without success - @x, @{x} ,
> x,
Bob,
That's certainly more straight forward than addition. I was just envisioning
situations where an individual atom is deleted, and a user wants to add some
atom back in. Creating a quarternary nitrogen would also require addition of
a new atom.
At this point, via click, I can replace atoms, ch
I think you should always be able to know where the atom is to go. If it
were me, I would always do atom replacement, so when, say, I click on an H
atom, it becomes a CH3. Isn't that the way Spartan does it? I would just
follow their lead on that. No need to reinvent the wheel here.
Bob
On Fri, F
Otis Rothenberger schrieb:
> Rolf,
>
> Yup, that seems to work for getting the atomIndex. It just took a while
> for me to find the correct dot notation by playing with:
>
> var z={*}.atomIndex.max;echo @z;
>
> I'm new to the math component of Jmol, so I'm doing a lot of trial and
> error with
Rolf,
Yup, that seems to work for getting the atomIndex. It just took a while for
me to find the correct dot notation by playing with:
var z={*}.atomIndex.max;echo @z;
I'm new to the math component of Jmol, so I'm doing a lot of trial and error
with math notation right now.
I have not tried you
Otis Rothenberger schrieb:
> Subsequent methylamine to ethylamine adds the carbon atom, but it will
> not connect, nor will it add hydrogens. Checking all three atomInfo's
> shows the problem. There is atomIndex confusion with all the deleting
> and adding going on. The array lengths are correct
Bob and Rolf,
A fairly lengthy data list is appended to this email.
It looks like atomIndex assignment has problems with my approach. The
JavaScript function is now:
function appendC(x) {
var scpt = "select;var z={*}.length;set appendNew false;data
'append'|1|add|C 5 5 5|end 'append';show da
Thanks Bob and Rolf.
{*}.length to get the atomIndex of the appended atom makes the embarrassing
astatine trick go away. It also has some general utility.
Bob, putting the appended atom anywhere in the reach of other atoms seems to
always get it mired in a web of strange bonds after "minimize add
On Thu, Feb 18, 2010 at 11:20 PM, Otis Rothenberger wrote:
> Hello-
>
> I'm working on an atom append script to click append a C atom (methyl group
> actually) to an existing atom in a Jmol model. The following JavaScript
> function works, but it is far from elegant. I'm fairly sure that there are
On 02/19/2010 06:20 AM, Otis Rothenberger wrote:
> 1) The ridiculous addition of astatine relates to my inability to use
> getProperty for the atomIndex of the newly appended atom, so I appended a
> very rare element, selected it, and changed it to carbon. Is there a way to
> get this atomIndex a b
On 02/19/2010 11:19 AM, Rolf Huehne wrote:
> I am not sure if I understand what the problem is here.
> Is it that you want to display everything except the appended atom at
> "50 50 50" filling the view?
> If this is the problem you could try "zoomto (atom expression)".
>
Sorry, I forgot the impor
On 02/19/2010 06:20 AM, Otis Rothenberger wrote:
> Hello-
>
> I'm working on an atom append script to click append a C atom (methyl group
> actually) to an existing atom in a Jmol model. The following JavaScript
> function works, but it is far from elegant. I'm fairly sure that there are
> Jmol ma
Hello-
I'm working on an atom append script to click append a C atom (methyl group
actually) to an existing atom in a Jmol model. The following JavaScript
function works, but it is far from elegant. I'm fairly sure that there are
Jmol math approaches to deal with some specific script actions that
Thanks to everyone for helping with this. I understand where I was
going wrong and I've got things in much better shape now. I have
another question. I've pulled data out of the file loaded into Jmol
and used it to plot points in an svg element. I would like to use
jQuery to access thos
Interesting idea. Probably without the points would be nicer.
On Wed, May 27, 2009 at 4:43 PM, Xavier Prat-Resina wrote:
> Not sure if it's useful, I'm using jQuery/flot here
> http://www.chemeddl.org/collections/molecules/index.php
> click the IR spectrum button and a flot chart pops up
>
> Xavi
Not sure if it's useful, I'm using jQuery/flot here
http://www.chemeddl.org/collections/molecules/index.php
click the IR spectrum button and a flot chart pops up
Xavier
On Wed, May 27, 2009 at 3:37 PM, Robert Hanson wrote:
> Jeff, I'm using jQuery at
>
> http://chemapps.stolaf.edu/jmol/docs/exa
Jeff, I'm using jQuery at
http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot.htm
and
http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm
I'm sure your problems do not arise from Jmol.js. The jQuery business is
quite well modularized.
Bob
On Wed, May 27, 2009 at 11:
Andreas,
It looks to me like some kind of timing issue. I've made a page with
some jQuery stuff on it. It works. I add a Jmol applet. Everything
still works. I then put a function that grabs data from the Jmol
applet inside the (document).ready wrapper and put a call to that
function
Hi Jeff,
Now sure what's exactly the problem from your description, perhaps you
can send some example code?
We are using a mix between JQuery and self written javacript on the
new RCSB-PDB web site:
e.g. this page tracks the Jmol console output to a div and shows the
command history:
http://www.
Does anyone have any experience using jQuery on a page with Jmol? I
wanted to do this as it would greatly simplify some things I wanted to
do. Unfortunately, none of the jQuery seems to be working. Let me
explain. I can load a Jmol applet and structure and write javascript
to manipulate
For small molecules, you can use this website :
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
It allows to design small molecules through the JRE applet and
calculates a minimized energy model.
Other websites such as Klotho or Drugbank are great for organic molecules.
Paul
David Kim a écrit
David, you might also be interested in a site we developed here at St.
Olaf, as it has about 1000 small molecules;
http://www.stolaf.edu/depts/chemistry/mo/struc/
with associated model files in
http://www.stolaf.edu/depts/chemistry/mo/struc/data/
Bob Hanson
David Kim wrote:
> Hello,
>
> My
(I have answered to David through the developers list)
-
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Hello,
My name is David Kim and I am currently an employee of the National Center
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