I'm certainly not seeing that. I do see that they don't have the rwb
colorscheme. So coming from the JVXL file you need to specify the color
scheme:
isosurface t2.jvxl colorscheme "rwb"*
*I realize that should not be necessary, but it is. The color scheme used is
not saved with the isosurface in
Hi Robert,
Sorry it took me so long to answer. Your algorithm worked just fine, thank
you!
However, i'm having another trouble now. After the surface is generated
everything is alright, i save it as a .jvxl file, then when i try to load it
to the same molecule, the surface and the molecule don't
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
configurat
Thanks a lot, Bob!
Speaking on the application, it's an implementation of one spatial protein
structure modeling approach. We need to draw some geometric figures
(dodecahedron for instance) near the protein. Besides, we need an ability to
rotate and to move figures by user.
21:35 Wednesday 23 F
>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
>lowe
If you can make your polygon using atoms, you can move and rotate it
independently in quite interesting ways. That's actually a nice idea. Also,
though, you might consider using the PMESH command rather than DRAW. A pmesh
object can be rotated, and offset easily. One catch, I think, is that if it
h
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 th
Please try the latest upload of
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
I recently discovered Jmol wasn't extracting charge info from Spartan files;
this should be fixed for the next release and I think is there already in
that zip file version.
Thanks,
Bob
On Wed, Feb 23, 2
Johannes-
I'm afraid I can't help, but I can confirm what your seeing:
1) Your file does not display MEP in 12.1.35.
2) A water molecule mol2 file that I created in Accelrys does not display
MEP in 12.1.35
3) A water molecule Spartan file not display MEP in 12.1.35
4) The following PubChem file
Hi all.
I have a problem with water molecule electrostatic potential surface in
latest Jmol versions.
*Example:*
When I try visualize them using Jmol 11.x.xx versions, everything works
fine, but 12.x.xx versions won't show it.
All other molecules works just fine in 12.x.xx versions. Water m
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
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
Evgeny,
Yes, you can add dummy atoms using a script. See
http://www.mail-archive.com/jmol-
us...@lists.sourceforge.net/msg16573.html
for some more info and an example.
You should best use the existing "Xx" notation for an undefined
element. Then you can "select Xx" to act on it, set its size, co
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