On Fri, May 31, 2013 at 4:27 PM, Pshemak Maslak wrote:
> On 5/31/2013 5:04 PM, Robert Hanson wrote:
>
> In other words, it's Joules.
>
> The numbers displayed are NOT in Jules. (it is e^2 (au)/d (angstrom)).
>
No, of course not. I have no idea what I was referring to there.
>
>
>
> If th
Rick,
1) that "error" is just a test we do to check the browsers. You would think
that try/catch would avoid that message, but it doesn't. I don't know why.
Just ignore that.
2) you are probably reading binary files from a local machine or binary
files from a server without having the necessary P
On 5/31/2013 5:04 PM, Robert Hanson wrote:
In other words, it's Joules.
The numbers displayed are NOT in Jules. (it is e^2 (au)/d (angstrom)).
If the charges in the file are in atomic units (multiple of electron
charge) and the distances are measured in angstroms the Jmol
calculated value
>This was a Java2Script compiler error. I thought I had worked around all of
>those, but this was the first test of old-style JVXL file reading, I guess.
>Thanks, Rick!
>
>http//chemapps.stolaf.edu/jmol/jsmol.zip
>
>Bob
Thanks Bob, I got the JVXL files working! Unfortunately I have run into
In other words, it's Joules.
If the charges in the file are in atomic units (multiple of electron
charge) and the distances are measured in angstroms the Jmol calculated
values of electrostatic potential can be converted into kcal/mol by
multiplying by 332.
>
> I think that is what Jmol does wit
On May 31, 2013, at 9:49 AM, jmol-users-requ...@lists.sourceforge.net wrote:
> Message: 3
> Date: Fri, 31 May 2013 11:35:48 -0500
> From: Robert Hanson
> Subject: Re: [Jmol-users] Wikis using JSMol?
> To: "jmol-users@lists.sourceforge.net"
>
> Message-ID:
>
> Content-Type: text/plai
On 5/31/2013 2:02 PM, Pshemak Maslak wrote:
On 5/30/2013 9:22 AM, Robert Hanson wrote:
It's whatever units come from this calculation:
public float valueFor(float x0, float d2, int distanceMode) {
switch (distanceMode) {
case ONE_OVER_D:
return (d2 == 0 ? x0 * Float.POSITIVE_IN
On 5/30/2013 9:22 AM, Robert Hanson wrote:
It's whatever units come from this calculation:
public float valueFor(float x0, float d2, int distanceMode) {
switch (distanceMode) {
case ONE_OVER_D:
return (d2 == 0 ? x0 * Float.POSITIVE_INFINITY : x0 / (float)
Math.sqrt(d2));
c
Well, if you can use Jmol.js some way then you can use Jmol.js the same
way. ;)
On Fri, May 31, 2013 at 11:49 AM, Angel Herráez wrote:
> > I have a file that can be slipped in for Jmol.js that makes older
> > pages work as JSmol. Wouldn't that work?
>
> Oh, it might work.
>
> > What does Java v
On 31 May 2013, at 17:35, Robert Hanson wrote:
> I have a file that can be slipped in for Jmol.js that makes older pages
> work as JSmol. Wouldn't that work? What does Java vs JavaScript have to do
> with the fact that it is a wiki? (unless there's a jQuery incompatibility,
> I suppose).
>
It
> I have a file that can be slipped in for Jmol.js that makes older
> pages work as JSmol. Wouldn't that work?
Oh, it might work.
> What does Java vs JavaScript
> have to do with the fact that it is a wiki?
Basically, you cannot insert javascript code in the wiki page. It all
has to be done
I have a file that can be slipped in for Jmol.js that makes older pages
work as JSmol. Wouldn't that work? What does Java vs JavaScript have to do
with the fact that it is a wiki? (unless there's a jQuery incompatibility,
I suppose).
On Fri, May 31, 2013 at 8:45 AM, Angel Herráez wrote:
>
> >
This was a Java2Script compiler error. I thought I had worked around all of
those, but this was the first test of old-style JVXL file reading, I guess.
Thanks, Rick!
http//chemapps.stolaf.edu/jmol/jsmol.zip
Bob
On Thu, May 30, 2013 at 1:58 PM, Spinney, Richard <
rspin...@chemistry.ohio-state.ed
On 31 May 2013, at 14:45, Angel Herráez
wrote:
>
>> You just flip the switch in Info from use:"Java" to use:"HTML5".
>
> I don't think so. The existing information for Wikis will use either
> Jmol.js
Yes, and a custom extension for Mediawiki.
> or, most likely, wiki-engine-specific extensi
> You just flip the switch in Info from use:"Java" to use:"HTML5".
I don't think so. The existing information for Wikis will use either
Jmol.js or, most likely, wiki-engine-specific extensions that
implement Jmol applets.
So, description(s) for the new Jmol-JSO method (either Java or HTML5
JSm
On Fri, May 31, 2013 at 7:30 AM, Greeves, Nick wrote:
> Hi Bob,
> I must have stumbled into this functionality without realising it wasn't
> official yet!
>
> I had created http://138.253.125.70/~ng/Demo/jsmol/galleryIPython.htmland
> noted that JSMol seems to "flatten" PyMOL frames into a sing
Nick,
Ah, frames and models. It's more interesting than that. Here is the
correlation:
PyMOL object --> Jmol selectable/displayable atom set, isosurface, CGO
(also new to Jmol), or measurement
PyMOL state --> Jmol MODEL
PyMOL frame --> new Jmol FRAME option
PyMOL movie --> new Jmol ANIMATION opti
Hi Bob,
I must have stumbled into this functionality without realising it wasn't
official yet!
I had created http://138.253.125.70/~ng/Demo/jsmol/galleryIPython.html and
noted that JSMol seems to "flatten" PyMOL frames into a single model. In this
example (not mine) I think the substrates are
Dear Jmol users,
The driving force behind these last four months of Jmol/JSmol development
has been e-publication. The goal has been to produce a means of
e-publishing working interactive biomolecular models that are ubiquitously
accessible (i.e. no Java, no WebGL). We achieved that goal for Jmol
I don't see any "excellent description there", but it's exactly the same
now.
You just flip the switch in Info from use:"Java" to use:"HTML5".
Bob
On Fri, May 31, 2013 at 5:37 AM, Rzepa, Henry S wrote:
> This excellent page;
> http://wiki.jmol.org/index.php/Wikis_Using_Jmoldocuments how to i
This excellent page; http://wiki.jmol.org/index.php/Wikis_Using_Jmol documents
how to integrate the Java-based Jmol into wikis. Is there a concise
description of how to achieve the same effect using JSMol?
Apologies if the list has already discussed this (the activity is so high I
have d
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