A case of odd outcome.
I have run the following in 12.0.11 and 12.1.9 (and compared to 12.0,8
which I happen to have on my website)::
isosurface cutoff 0.09 resolution 5 phase color
translucent 7 atomicOrbital 2 0 0 1.0
One would expect three concentric isosurface
Here is my report.
PM*
12.0.11 and 12.1.9: no differences in performance observed
*
# bug fix: failure to read old-style JVXL files.
works fine, old file read correctly
# bug fix: isosurface contour colors, contours, and drawHover
set drawHover true; isosurface color absolute -0.01 0.9
I placed the
command in the wrong order, although I tried several with no error
message in the console, but without any effect on the surfaces drawn.
Thank you.
PM
On Wed, Sep 1, 2010 at 7:58 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
BTW: Does squared
On 8/30/2010 6:33 PM, Robert Hanson wrote:
Pshemak, thanks very much for that excellent list.
Run-times. I'm pretty sure this is isolated specifically to atomic
orbitals. It has to do with the size of the box used to create the
grid. Jmol 11.8.24 had a bug that sometimes truncated
On 8/30/2010 5:21 PM, Robert Hanson wrote:
ps. 12.0 adds dsp3 and d2sp3
2010/8/30 Angel Herráez angel.herr...@uah.es
mailto:angel.herr...@uah.es
On 30 Aug 2010 at 9:26, Pshemak Maslak wrote:
Is there a way to display hybrid orbitals in Jmol? I am thinking at
least about sp3
On 8/31/2010 3:49 PM, Robert Hanson wrote:
On Tue, Aug 31, 2010 at 11:07 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
Why is there a hole in the middle of 1s orbital wavefunction?
Because the data are from a grid, and the grid has no information
there. I've
I am afraid that some things did not get resolved in the new versions.
Below is the list.
PM
Run-times (approximate, from pressing run till surface is shown, all
on the same desktop computer, no server involved)
isosurface peskin3 cutoff 0.05 resolution 3 phase color darkred darkblue
On 8/29/2010 8:28 PM, Robert Hanson wrote:
Definitely not set up for Fischer projections.
Calculate Hydrogens was just broken on my local copy where I was
working on implementing sp3d and sp3d2 hybridization and {...}.shape
(tetrahedral, trigonal planar, T-shaped, etc.)
Bob
Is there a
On 8/26/2010 8:08 AM, Robert Hanson wrote:
Pshemak,
Jmol 12.0.9, just released, doesn't fix the problem with atomic
orbitals. Actually, it made it worse. Sorry about that! I forgot to
test it with radial functions that approach 0 from below at infinity.
The next release will fix that; I'll
On 8/24/2010 6:57 PM, Robert Hanson wrote:
On Tue, Aug 24, 2010 at 3:45 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 8/24/2010 4:28 PM, Robert Hanson wrote:
Has anyone tried this?
isosurface molecular map mo homo
It seems to me
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
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
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 just replaced version 11.8 with 12.08. Since I am still very new
12.0 (and beyond); just need more time to get some basics.
Thanks,
PM
On Wed, Jul 21, 2010 at 7:55 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 7/20/2010 7:27 PM, Robert Hanson wrote:
to draw the isosurface you need to use the isosurface command
to learn and it appears
that Jmol is being developed faster than I am learning it :-)
PM
On Tue, Jul 20, 2010 at 12:38 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 7/20/2010 1:24 PM, Angel Herráez wrote:
Pshemak, you have a problem with quotes --at least
More beginner's questions:
What is the correct syntax to display the isosurface from the loaded
file (part of image map link). I believe the problem is with the
quotation marks. The file (allyl-MO-3.jvxl is in the /models
subdirectory. The file loads the structure fine, but not with the
On 7/20/2010 1:24 PM, Angel Herráez wrote:
Pshemak, you have a problem with quotes --at least--
href=javascript:jmolScript('load models/allyl-MO-3.jvxl; isosurface ;')
the quote after isosurface is closing the quote after href
You need to escape the quotes:
I have a beginner question:
How do you link pictures to actions in Jmol on the same page? Is there a
jmolLink equivalent for pictures?
Thanks,
PM
--
This SF.net email is sponsored by Sprint
What will you do first with
On 7/13/2010 8:58 AM, Alexander Rose wrote:
Hi,
untested idea:
jmolLink(script, 'img src=path/to/image.png /', id, title)
Alex
Now it is tested. It works. Thanks!
PM
- Ursprüngliche Mail -
Von: Pshemak Maslak p...@chem.psu.edu
An: jmol-users@lists.sourceforge.net
On 7/13/2010 9:04 AM, Angel Herráez wrote:
jmolLink(script, 'img src=path/to/image.png /', id, title)
If that doesn't work, you can also do:
img src=path/to/image.png onClick=jmolScript('spacefill on') /
More beginner's questions:
I am sure, I am missing something obvious. How
...@lists.sourceforge.net
mailto:jmol-users-requ...@lists.sourceforge.net wrote:
Date: Tue, 13 Jul 2010 08:52:03 -0400
From: Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu
Subject: [Jmol-users] picture linking to Jmol
To: jmol-users@lists.sourceforge.net
mailto:jmol-users@lists.sourceforge.net
Message-ID
On 6/30/2010 4:50 PM, Robert Hanson wrote:
I'm not having that problem at all with my Spartan files. I look at a
vibration:
frame 3; vibration on
then go back to frame 1 and check the MO:
frame 1; MO HOMO
Works fine. Certainly Jmol is never no longer able to access Frame 1.
Maybe you
On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 6/25/2010 4:51 PM, Greeves, Nick wrote:
I have used smol files for vibration
e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well
without any server side settings
, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:
On 6/29/2010 7:20 PM, Robert Hanson wrote:
I'll look into the mep/mo business. Should not be a problem. Just
a bug, I think.
Thank you very much for your help.
I do have two related
...@depauw.edu mailto:jhan...@depauw.edu
***
On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote:
On 6/30/2010 9:32 AM, Robert Hanson wrote:
When Jmol reads a Spartan smol file, it accesses all vibrations and
all molecular orbitals (supposedly!) They should
On 6/30/2010 2:33 PM, Jeff Hansen wrote:
Glad that helped. Making it easily accessible to students means doing
most of the work for them. In the case of Jmol that means setting up
buttons or checkboxes or whatever user interface then scripting what
you want the students to see. In the
On 6/25/2010 4:51 PM, Greeves, Nick wrote:
I have used smol files for vibration
e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well
without any server side settings.
All the best
Nick
Sent from my iPad
Thank you very much for the example. Your case indeed clarifies the
Hello to everybody!
I am a new Jmol user and would like to learn more about smol files
(Spartan, Wavefuction)
The specific questions I have are:
1. What is the MIME type for smol files to be correctly read on a server?
2. The smile files may contain several surface data (MO, densities of
On 6/25/2010 1:35 PM, Angel Herráez wrote:
Hello, PM
I am a new Jmol user and would like to learn more about smol files (Spartan,
Wavefuction)
Maybe this is not the best place to ask. You should address some Spartan
community
Thank you for your suggestion.
Obviously, I would
On 6/25/2010 2:42 PM, Angel Herráez wrote:
It is probably true on a desktop, but I do not think this is correct on a server. If a MIME type is not
set, a file like.smol (or even jvxl) will not be read by the web app.
I'm quite sure of this: Jmol does not care about MIME type. It may be
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