I'm trying to feed GET returns from the NIH Chemical Identifier Resolver
directly to Jmol without using the signed applet. My reasons for wanting
to do this are not just Jmol related. I need to be able to feed other
NIH data to JavaScript on my page - a JavaScript security violation
under norma
On Tue, Aug 24, 2010 at 9:38 PM, Otis Rothenberger wrote:
> Bob,
>
> You can check me on the alpha-D-talose. I've been known to show the same
> aldose confusion as some of my students.
>
>
I'm pretty sure it's alpha-L-talose. The point is that like so many of these
databases, they are not defin
Bob,
We've been working on a Fisher configuration proof student model
exercise using Jmol compare to have students follow the identity of the
aldoses as they hack away at glucose from the top down. Consequently, we
have good aldose SMILES and coordinates in an internal database. From
this, I
sorry bug there...
smilesUrlFormat = "
http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True
";
for now
On Tue, Aug 24, 2010 at 6:53 PM, Robert Hanson wrote:
> You can do this yourself using
>
> set smilesUrlFormat "
> http://cactus.nci.nih.gov/chemical/structure/%FILE
You can do this yourself using
set smilesUrlFormat "
http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True
";
and then the load commands below will work.
On Tue, Aug 24, 2010 at 6:41 PM, Robert Hanson wrote:
> oh my oh my oh my
>
> I've changed the SMILES server ur
oh my oh my oh my
I've changed the SMILES server url in 12.1 to this NIH server because it is
so very fast and I am SO impressed -- superb conversion to 3D, even for
steroids. Stereochemistry is good, conformation is good. Allene
stereochemistry is missing, but incorrect SMILES bond stereochem
On Tue, Aug 24, 2010 at 3:45 PM, Pshemak Maslak wrote:
> On 8/24/2010 4:28 PM, Robert Hanson wrote:
> > Has anyone tried this?
> >
> > isosurface molecular map mo homo
> >
> > It seems to me that's an interesting way to see where a model might
> > react.
>
>
> > Bob
>
> Both HOMO and LUMO map
On Tue, Aug 24, 2010 at 3:45 PM, Pshemak Maslak wrote:
> On 8/24/2010 4:28 PM, Robert Hanson wrote:
> > Has anyone tried this?
> >
> > isosurface molecular map mo homo
> >
> > It seems to me that's an interesting way to see where a model might
> > react.
> >
> > Bob
>
> Both HOMO and LUMO maps
On Mon, Aug 23, 2010 at 8:41 AM, Pshemak Maslak wrote:
> Hello,
>
> First of all Jmol is an amazing program and I am extremely impressed by
> its rapid growth since I started using it about two moth ago. I have
> difficult time keeping up with the updates. Kudos to the developers!
>
>
> I have j
On 8/24/2010 4:28 PM, Robert Hanson wrote:
> Has anyone tried this?
>
> isosurface molecular map mo homo
>
> It seems to me that's an interesting way to see where a model might
> react.
>
> Bob
Both HOMO and LUMO maps of that kind are "standard" tools in Spartan,
occasionally quite useful in
Has anyone tried this?
isosurface molecular map mo homo
It seems to me that's an interesting way to see where a model might react.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
Indeed!
set rotationRadius (Angstroms)
*Sets the nominal rotation radius for the model effectively setting the size
of the model at zoom 100. Normally set to the radius that will contain
within the screen the entire model when rotated relative to the default
rotation center.
*
:)
Bob
On Mon,
On Mon, Aug 23, 2010 at 11:01 AM, Shore, Jay wrote:
>
> I really like jmol’s multiple bond representation – it is the only
> visualization tool that I know of that actually
> that actually does multiple bonds.
>
> The distance between the cylinders (that represent a double bond) changes
> when th
We think 12.0.1-12.0.7 had a bug that made it so that Jmol would not start
for new users (so with no history file)
That was fixed in 12.0.8, I thought.
On Tue, Aug 24, 2010 at 12:31 PM, Jonathan Gutow wrote:
> Tim,
>
> First try starting by just double clicking on Jmol.jar...The Jmol.bat
> file
I'll look into it. I've been wondering about that myself, and now I have a
good way to test it. Thanks.
On Tue, Aug 24, 2010 at 12:49 PM, Pshemak Maslak wrote:
> I have reported in my previous e-mail that 12.0.8 (12 for short) is
> significantly slower than 11.8.24 (11.8 for short).
>
> I have
version=12.1.7_dev
# new feature: zSlab, zDepth -- default 0,0; when equal, it means "use slab
and depth" settings
# new feature: slab and depth are variables and can be read and set as for
any other
On Mon, Aug 23, 2010 at 2:55 PM, Thomas Stout wrote:
>
> I would second that vote!
>
> Cheers,
I have reported in my previous e-mail that 12.0.8 (12 for short) is
significantly slower than 11.8.24 (11.8 for short).
I have run a couple of simple scripts on an older computer directly on a
desktop (no web-server involved). I have used an older windows xp
machine 2.66 Ghz 4 GB memory Intel
Tim,
First try starting by just double clicking on Jmol.jar...The Jmol.bat
file probably hasn't been updated in a long time as Windows now
starts jar files with a double click.
Then try updating your Java version. There were some buggy initial
releases of 1.6. I think they are beyond 1.6
oh -- exit also clears all pending timeOut scripts...
On Tue, Aug 24, 2010 at 11:39 AM, Robert Hanson wrote:
> Eric, here's the scoop.
>
> There are a few undocumented features of quit and exit, and yes, there was
> a change there. (That we can certainly undo.)
>
> Right now:
>
> from the comman
Eric, here's the scoop.
There are a few undocumented features of quit and exit, and yes, there was a
change there. (That we can certainly undo.)
Right now:
from the command line:
"exit" clears he script queue, stops all processes, including scripts,
spinning, and minimization.
"quit" stops any
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