Might I suggest the CSD teaching set?
http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/CSDTeachingDatabase.aspx
This would save a lot of legwork, and I imagine they would be happy to
have the added value.
- Noel
On 30 September 2013 04:36, Geoffrey Hutchison wrote:
>> if there are open so
t, but probably would be useful to resolve (or not) this issue.
- Noel
On 5 March 2013 12:42, Marcus D. Hanwell wrote:
> On Tue, Mar 5, 2013 at 4:24 AM, Noel O'Boyle wrote:
>> Hey there,
>>
>> I used an automated GUI tester to investigate where Avogadro
Hey there,
I used an automated GUI tester to investigate where Avogadro accepts
clicks on a hydrogen:
http://baoilleach.blogspot.co.uk/2013/03/avogadro-hydrogen-clicking-craziness.html
(see comments there also for a discussion of the issues).
I would argue that the centre of the hydrogen is the l
To be clear, are you asking why MMFF94 is so poor at predicting dipole moments?
- Noel
On 19 January 2013 17:31, Steven Petrovic wrote:
> Hello,
> Despite how wonderful I think Avogadro is for molecular modeling and its
> potential for educational purposes, I hesitate to use Avogadro in the
> ch
Hello Avogadro developers,
I have just seen the Avogadro paper has been accepted by J Cheminf and
is available online in early form:
http://www.jcheminf.com/content/4/1/17/abstract
Congratulations to all involved, and continued success in the future.
All the best,
Noel
--
I have a GAMESS/Avogadro/MacMolPlt tutorial at
http://www.redbrick.dcu.ie/~noel/GAMESS_Apr2011/index.html.
See also this tutorial,
http://www.d.umn.edu/~psiders/courses/chem4642/quantumchemsoftware/tutorial/tutorial.html,
by Paul Siders at Univ Minnesota Duluth.
- Noel
On 16 May 2012 20:56, Geof
Hey there,
I know that the forcefields only cover certain atoms (or is it atom
types?) and so setup will fail in some cases.
But shouldn't the setup work if I set a problem atom as "fixed", or
even "ignore"? This would be useful for preparing QM calculations
where I have some exotic metal centre,
Maybe a "Highlight dodgy valences using halos" would be a useful engine...
On 21 December 2011 18:50, Geoff Hutchison wrote:
>> As we teach our students that oxygen has a valence of 2, it is annoying
>> that they can make a molecule where it has four chemical bonds ;o((
>
> Let me be clear that t
On 19 December 2011 19:54, David Lonie wrote:
> On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison
> wrote:
>>> Is there currently a GUI-based method to generate and view
>>> conformations of a molecule? Using the forcefield extension, I appear
>>> to be generating the conformers, but in View >
Actually it seems to be working now :-) My only problem is that I
can't figure out exactly why it was failing before...
- Noel
On 17 November 2011 15:55, Noel O'Boyle wrote:
> Hi all,
>
> I've been successfully usnig basic Signals from PyQt (Avo 1.0.1+Python
> on Wind
Hi all,
I've been successfully usnig basic Signals from PyQt (Avo 1.0.1+Python
on Windows) but I'm ready to throw in the towel on using signals with
parameters:
I have a QTableWidget and am trying to catch the signal when someone
clicks on a cell:
QObject.connect(self.allpharmas,
Hi there,
I've been working on a Python Engine that will display a pharmacophore
(basically a set of spheres in 3D space). I was hoping to make the
spheres transparent but it seems like this is not possible. Is this
correct?
Firstly, renderTransparent is not available in PythonEngine (not that
I'
Hi there,
I seem to be stuck using Avogadro 1.0.1 on Windows due to the lack of
a Pythonified binary. Any chance of this being made available?
Regards,
Noel
--
AppSumo Presents a FREE Video for the SourceForge Communi
Can it be true? An Open Source DFT code for small molecules!
- Noel
On 12 July 2011 14:40, Jussi Lehtola wrote:
> Hi,
>
>
> I'm working on implementing some new features in my SCF code called
> ERKALE ( http://erkale.googlecode.com ; new developers are warmly
> welcome!). Related to this, I
I did something similar a while ago, and described the process at the
following link:
http://baoilleach.blogspot.com/2010/04/plug-cclib-into-avogadro.html
I dd need to use Open Babel directly though, as I couldn't access the
Open Babel bindings in Avogadro (this was 1.0.0 on Windows).
- Noel
You should "make install" before attempting to use Open Babel. You can
do this locally if you configure CMake with
"-DCMAKE_INSTALL_PREFIX=/home/user/whatever", and then set
LD_LIBRARY_PATH appropriately.
- Noel
On 24 May 2011 11:02, Jaap Kroes wrote:
> Dear prof. Hutchison,
>
> Thank you for yo
On 19 May 2011 13:35, Archambault Fabien
wrote:
> My trial is on a water molecule (h2o.xyz):
> $ python
> >>> import Avogadro as a
> >>> mol = a.MoleculeFile.readMolecule('h2o.xyz')
> >>> for atom in mol.atoms:
> ... print atom.pos
> ...
> [ 0.00369 2.73505 2.63908]
> [-0.88715 2.29885
Clicking on the British flag at the top of the page goes to
http://www.univ-reims.eu/, instead of the English version. Apart from
that, looks good.
- Noel
On 11 March 2011 10:20, Mickaël Gadroy wrote:
> I create an english part in the WiiChem website (thanks to Noel O'Boyle) .
> Now
s widely in high schools as in
universities.
On 9 March 2011 16:24, Mickaël Gadroy wrote:
> That's a good idea. It will help me a lot.
> Thanks you in advance.
>
> Mickaël Gadroy
>
>
>
> 2011/3/9 Noel O'Boyle
>>
>> That is so cool.
>>
>> I think i
That is so cool.
I think it could be useful to make an English translation available -
will I give it a go, and send you the text?
- Noel
On 9 March 2011 15:56, eric henon wrote:
> Dear alls,
>
> We are please to announce that
> it is now possible to carry out the Wiimote possibilities
> into
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