got it! thanks. Xavier Prat-Resina wrote:
> 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? OK, that's in for 11.6.RC2 set pointGroupDistanceTolerance (default 0.2 angstroms) set pointGroupLinearTolerance (default 8 degrees) > 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] > <mailto:[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]> > > <mailto:[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]> > <mailto:[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/ > > > > > > > > > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move > Developer's > > challenge > > Build the coolest Linux based applications with Moblin SDK & win > > great prizes > > Grand prize is a trip for two to an Open Source event > anywhere in > > the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > <http://moblin-contest.org/redirect.php?banner_id=100&url=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/>> > > _______________________________________________ > > Jmol-developers mailing list > > [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > > > > > > -- > > 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> > <http://chem.wisc.edu> ; skype: > > xavierprat > > http://x.prat.resina.googlepages.com > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >This SF.Net email is sponsored by the Moblin Your Move > Developer's challenge > >Build the coolest Linux based applications with Moblin SDK & win > great prizes > >Grand prize is a trip for two to an Open Source event anywhere in > the world > >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Jmol-developers mailing list > >[email protected] > <mailto:[email protected]> > >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > > > -- > 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 > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > _______________________________________________ > Jmol-developers mailing list > [email protected] > <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > -- > 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 > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- 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 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
