That's pretty much what I figured in terms of one value compensating for
another. In terms of total energy though, even that doesn't seem reliable,
at least not in real world terms of kcal/mol -- perhaps relative to other
values from the same force field it is fairly consistent. If only ab initio
c
Hi Bob,
This is helpful as I wasn’t sure if I understood the intent.
I’ll do some more testing with my app in the next day or so to make sure that I
can reproduce what I’m seeing and create a generic example. There is still a
pretty good possibility that the bug is in my code.
The first larger
http://chemapp.stolaf.edu/jmol/zip/jmol-14.1.11_2014.02.24.zip
Should fix Otis's minimization problem in HTML5 for 14.1.11
Adds standard JavaScript-like array element access for Jmol scripting and a
more JSON-like definition syntax:
a = [testing:"one",again:"here", b:[ [more:"here"], 2, 3] ]
p
It's definitely supposed to stop. The rotation is a separate process, so it
is supposed to be continuing after the script is "finished". I'm not able
to reproduce your problem. -- Can you put up a page that illustrates that?
On Mon, Feb 24, 2014 at 3:35 PM, Charles Harrison Shubert
wrote:
> JSm
I've added show minimization to the next upload of the documentation.
Thanks.
You have to remember that this is a huge set of parameters that were
optimized for a specific data set. I would refer you to the literature
reference. Mostly you cannot get anything significant from any one
parameter, an
the "system" one is for JSmolCore.js
the "Jmol" one is for the j2s and java directories. Quite possible that
they will be different.
On Mon, Feb 24, 2014 at 9:29 AM, Otis Rothenberger wrote:
> I'm in a bit of version flux right now, buy a see a slightly different
> result for ?? replacement on
yes, indeed. It's HTML5 only; missing the Measures.js component in
coretext.z.js
I'll get that build again soon.
On Mon, Feb 24, 2014 at 12:48 AM, Otis Rothenberger
wrote:
> Bob,
>
> I think measure may be broken on this one - our VMK model kit scripts and
> Jmol right click menu. Maybe I had a
codepath is fine -- that's just for Jmol, not Java.
On Sun, Feb 23, 2014 at 2:04 PM, Angel Herráez wrote:
> Dear Bob,
>
> Jmol 14.0.10_2014.02.19
>
> I am setting up some pages with JSmol, this is loading fine. However,
> when I switch to Java in the URL, an error says blocked by Java securi
JSmol.min.js
___JmolDate="$Date: 2014-02-14 13:28:43 -0600 (Fri, 14 Feb 2014)
$";___fullJmolProperties="src/org/jmol/viewer/Jmol.properties";___JmolVersion="14.0.8";
Issue: zap does not seem to stop the rotation of a molecule that has been
zapped.
Here's what I do and see:
My app load a large
Thanks Robert, I figured it must be available somehow - almost everything
is :) I would mention thought that "show minimization" isn't in the docs
as far as I see at
http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=14.2#show. Good
thing to add, unless I just missed it!
That leaves me with
I'm in a bit of version flux right now, buy a see a slightly different result
for ?? replacement on the JSmol side. While the box does not check, if I go
back and "select" it again (still unchecked), the replacement works. Two
versions tested, but I must admit I'm a bit version confused with the
The problem I saw in the Java stand-alone seems to be fixed in
14.0.11_2014.02.21 where the system would lock up when any ModelKit action
was tried. !exit would then report "script execution halted with !exit"
but not resolve the lock up.
There is, however, still a problem. Although the ?? select
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