Bob,
the fix solved most of the problems, but it still doesn't find the plane
when all the atoms are contained in it
Hypochlorous Acid : C<sub>S</sub> : C1
http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=34
Hyponitrous Acid : C<sub>S</sub> : C1
http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=98
I have a question/request. When the algorithm looks for symmetry elements,
would it be useful to introduce a keyword to control the tolerance for
distance/angles
comparisons?
I can imagine that for experimental structures the tolerance should be
higher,
and the user might need to tune that.
Just a thought.
Xavier
On Wed, Aug 6, 2008 at 5:23 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> I just uploaded a fix -- should be good as SourceForge. And Nico just
> released a version, so please check that.
>
> Xavier Prat-Resina wrote:
>
> > Bob,
> >
> > this is a very nice tool!
> > I still don't see the solution to the problem that Jonathan pointed out,
> > I still get D3d for his BF3.PDB with version 11.6.RC1, is there any
> > other version?
> > I know you are still debugging, so I thought it might be useful to report
> > what seems to me some discrepancies between the symmetry computed by jmol
> > and the one computed by Patchovskii's code. In some cases jmol is better!
> > Here's a list of the molecules in which jmol failed to identify the
> > symmetry point group.
> > It seems that it doesn't find some planes.
> >
> > Name : patchovskii : jmol : link
> >
> > Chlorine Dioxide : C<sub>2V</sub> : C2h
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=13
> > Hypochlorous Acid : C<sub>S</sub> : C1
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=34
> > Nitrite Ion : C<sub>2V</sub> : C2h
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=41
> > Nitrogen Dioxide : C<sub>2V</sub> : C2h
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=43
> > Nitrous Acid : C<sub>S</sub> : C1
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=46
> > Oxygen Difluoride : C<sub>2V</sub> : C2h
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=49
> > Sulfur Dioxide : C<sub>2V</sub> : C2h
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=57
> > Sulfur Trioxide : D<sub>3H</sub> : D3d
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=60
> > Aluminum Chloride : D<sub>3H</sub> : D3d
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=79
> > Aluminum Fluoride : D<sub>3H</sub> : D3d
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=80
> > Chlorine Oxide : C<sub>2V</sub> : C2h
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=92
> > Hyponitrous Acid : C<sub>S</sub> : C1
> >
> http://www.chemeddl.org/collections/labs/avisualdatabase/index.php?molecule=98
> >
> > Xavier
> >
> >
> > On Wed, Aug 6, 2008 at 2:28 PM, Jonathan Gutow <[EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>> wrote:
> >
> > That seems to have fixed the problem. This is quite cool!
> > Jonathan
> > On Aug 6, 2008, at 1:06 PM, Bob Hanson wrote:
> >
> > > There we go.... I was checking only for planes perpendicular only
> > > to C2
> > > axes, not C3. Better?
> > >
> >
> > Dr. Jonathan H. Gutow
> > Chemistry Department
> > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> > UW-Oshkosh
> > Office:920-424-1326
> > 800 Algoma Boulevard FAX:920-424-2042
> > Oshkosh, WI 54901
> > http://www.uwosh.edu/faculty_staff/gutow/
> >
> >
> >
> >
> >
> >
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> >
> >
> > --
> > Xavier Prat-Resina
> > Research Associate
> > Journal of Chemical Education and University of Wisconsin
> > 209 N. Brooks St. Madison, WI 53715-1116
> >
> > Tel: 608 8901702 // Fax: 608 2627145
> > e-mail: xavier ( ) chem.wisc.edu <http://chem.wisc.edu> ; skype:
> > xavierprat
> > http://x.prat.resina.googlepages.com
> >
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>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
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--
Xavier Prat-Resina
Research Associate
Journal of Chemical Education and University of Wisconsin
209 N. Brooks St. Madison, WI 53715-1116
Tel: 608 8901702 // Fax: 608 2627145
e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com
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