Bob,
I can get the translated coordinates and frame adjustments from the state
script of your page, so I have no problem loading your adjusted data for
Hen's file. But I have looked at that file for years and said, Boy I'd
like to translate the those coordinates.
So, just as a Jmol learning
load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz
for (var i = 1; i 35; i++) { var j = i+1;compare {model=j} {model=i}
ROTATE TRANSLATE 0.0 }
There are 35 models. This runs through the models, rotating and translating
each model to be the best match to the previous model in the
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz
for (var i = 1; i 35; i++) { var j = i+1;compare {model=j} {model=i}
ROTATE TRANSLATE 0.0
--
*From*: Robert Hanson hans...@stolaf.edu
*Sent*: Monday, February 28, 2011 9:13 PM
*To*: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
*Subject*: Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip
demo
load http://wetche.cmbi.ru.nl/organic/cyclohexane
It sure would be a service to all organic students if someone were to create
a good, interactive web page that draws from Hens' page and shows using Jmol
the smooth transition from chair to chair via half-twist (I was calling this
twist-chair) and twist (I was calling this twist-boat) as well as
Henry, it took a little fixing of Jmol, but I was able to visualize the
symmetry there, and this is what I came up with:
The path takes us from D2d through C2 (twist chair) to D2 (twist boat) to C2
(twist chair) to D2d again. The plane of symmetry is broken immediately with
the first twist, and
On 23 Feb 2011, at 01:33, Robert Hanson wrote:
Well, at least I think so
http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol
Please let me know if that does not work for you.
Bob,
The issue of whether the path passes through a boat
Op 23-2-2011 10:12, Rzepa Henry schreef:
I appreciate a debate on this topic may or may not be suited for the
Jmol list, but if anyone wants to add their opinion, I would welcome
this, if only because my synthetic organic chemistry colleagues
need to know what the most realistic
Hens! Good to hear from you. I hope you don't mind my co-opting your model
-- reminds me that I need to put a link to WeTChe there.
I'd love a little discusson of this, because I'd like to get this out there.
My understanding is that both are correct -- the boat transition state is
lower than the
Henry, so you are saying you think something is wrong with that pathway.
From what I can see, there are two possible pathways from the chair -- one
with a twist to the left; one with a twist to the right. The
enatiomeric twist is not depicted. (Although I think you could invert the
configuration
Well, at least I think so
http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol
Please let me know if that does not work for you.
This is identical to the original from
http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxjmol.html produced by
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