Has anybody solved this one?
Gaussian computes an IRC by starting at the transition state (frame 1) and
following the IRC down to a rest in one direction (lets say frame 25), then
starting again from the geometry of frame 1 (this will now be numbered 26) and
computing the IRC in the
Henry,
I'm not sure if this helps your situation, but we run animations in our own
loop (e.g. below). You can pretty much do whatever you want with respect to
frame display:
var filePath = animations/Chlorination_of_anisoleF.TXT;
var frameInterval = .1;
load @filePath;hide *;background
Otis,
Chlorination_of_anisoleF.TXT contains what? A gaussian log file?
I think your script has 9 different start points, but they all proceed in a
positive direction from that point?
I guess I want to re-order the frames in a Gaussian file, ie show 57 to 26,
then immediately jump to frame 1
On 1 Feb 2014, at 19:54, Robert Hanson hans...@stolaf.edu wrote:
Robert Lancashire and I are happy to announce the first online open-source
fully JavaScript fully customizable 1D HNMR prediction tool. Perfect for the
classroom or for research laboratories,
Perfect indeed!
I do have one
Henry,
Sorry, I should have cut to the chase on what we're doing. The .txt file is a
multi-frame molfile. Rather than rely on Jmol animation modes, we run it frame
by frame ourselves. Cutting through my verbose specifics:
1) Load the animation file into Jmol.
Note on the above: You're thinking
On 2 Feb 2014, at 15:05, Otis Rothenberger osrot...@chemagic.com wrote:
Henry,
Sorry, I should have cut to the chase on what we're doing. The .txt file is a
multi-frame molfile.
Yes, so its up to the user to convert each Gaussian log file to a multiframe
molfile. In fact, since Jmol
Henry,
OK, I see what your saying. But I'm confused on one point. I don't think
conversion to molfile is required. Am I wrong on this point?
It seems to me that once the multi-frame file is in Jmol, a frame is a frame
(scripting-wise). Shouldn't something like the following work?
var filePath
When I replaced the j2s files with the ones of jmol-14.1.8
version, I could not see models in the HTML5+Javascript mode.
In the case of jmol-14.0.7, it does work well.
Is there any informations?
Please see
jmol-14.0.7_dev_2014.01.20
http://www3.u-toyama.ac.jp/kihara/jsmol/index.html
I would like to thank your quick response.
I found the bug was fixed with signed jar.
But the problem is remained with unsigned jar.
Please see
Unsigned
http://www3.u-toyama.ac.jp/kihara/jsmol3/mo.html
Signed
http://www3.u-toyama.ac.jp/kihara/jsmol3/mo-sec.html
--
(2014/01/29
George, did I mention that
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.02b.zip has a
tinker.xyz reader? You do have to prefix that, as there is apparently no
way to know this is a tinker file:
load tinker::.xyz
Henry, you can animate frames in any order now.
animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)]
I think I forgot to document that. It was introduced in Jmol 13.1.
Bob
On Sun, Feb 2, 2014 at 2:57 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote:
Has anybody solved this
You replaced all .js files in the main jsmol/ directory as well? Shouldn't
be a problem; send a URL to a problem page.
On Sun, Feb 2, 2014 at 8:07 PM, Hiroshi Kihara kih...@itc.u-toyama.ac.jpwrote:
When I replaced the j2s files with the ones of jmol-14.1.8
version, I could not see models in
sorry - didn't read far enough. Yes, the file you call Jmol.js file needs
to be re-created. JSmol.min.js will change with each distribution.
On Sun, Feb 2, 2014 at 8:07 PM, Hiroshi Kihara kih...@itc.u-toyama.ac.jpwrote:
When I replaced the j2s files with the ones of jmol-14.1.8
version, I
both are working; you just have to make sure when you make changes to the
Jar files that you also close your browser and start it again. Make sure
ALL windows are closed. Some browsers may not clear the Java cache even
then, and you have to go into the Java control panel and clear the cache
models[] is an array that starts with 1:
$ print getproperty(auxiliaryInfo.models[1].keys)
name
modelNumberDotted
fileHeader
modelNumber
fileName
dipole
modelFileNumber
moData
modelName
initialAtomCount
energy
Energy
modelProperties
initialBondCount
EnergyString
fileType
$ print
By the way, George, if you are going to do this in a loop, it is VERY much
more efficient to define variables as much as you can and not call
getProperty every time:
x = getProperty(auxiliaryInfo.models[1].modata.mos)
print x[21][energy]
print x[22][energy]
etc. Note that Jmol math needs to
I understand.
I really appreciate your kind explanation.
--
(2014/02/03 14:52), Robert Hanson wrote:
both are working; you just have to make sure when you make changes to the
Jar files that you also close your browser and start it again. Make sure
ALL windows are closed.
On 3 Feb 2014, at 05:42, Robert Hanson hans...@stolaf.edu wrote:
Henry, you can animate frames in any order now.
animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)]
I think I forgot to document that. It was introduced in Jmol 13.1.
Great! It is common nowadays
I understand I should have re-created Jmol.js file.
I really appreciate your kind explanation.
(2014/02/03 14:48), Robert Hanson wrote:
sorry - didn't read far enough. Yes, the file you call Jmol.js file needs
to be re-created. JSmol.min.js will change with each distribution.
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