Michael Sternberg wrote: >Bob, > >Thank you for the quick fix! I downloaded and tested 11.5.41. >Scalars with a decimal(!) are recognized as partial charges, and >"select" and "color" can operate on them. Great! > > > -- right -- I forgot to mention that integer in the 5th field of an xyz file are translated as formal charge, not partial charge. I figured this would not be an issue, as any program that generates partial charges will add the decimal even for integers. Correct me if I'm wrong.
The XYZ reader reads any of the following now: Sym x y z Sym x y z vibX vibY vibZ Sym x y z FormalCharge(int) Sym x y z FormalCharge(int) vibX vibY vibZ Sym x y z PartialCharge(decimal) Sym x y z PartialCharge(decimal) vibX vibY vibZ where Sym is either an element symbol (C, Fe, Si) or an element symbol preceded by an isotope number (2H, 13C, etc.) I believe this is sort of a bastardization of the original XMOL format. But I agree, it's a great format. What a lot of people probably don't realize is that you can even apply full symmetry (unit cells, symmetry operations) to this file format simply by adding UNITCELL and SPACEGROUP parameters to the LOAD command. In other words, you can "retrofit" simple xyz data to an original full-symmetry format. That is really a very powerful capability of Jmol. Bob >Regards, Michael > > >On Jun 16, 2008, at 13:15 , Bob Hanson wrote: > > > >>OK, that's in for 11.5.41. For some reason the reader was set up to >>round that charge. I consider it a bug. Fixed also for 11.4.5. >> >>Bob >> >> >> >>Michael Sternberg wrote: >> >> >> >>>On Jun 16, 2008, at 10:28 , Michael Sternberg wrote: >>> >>> >>> >>> >>>>I like the XYZ format for its simplicity and >>>>flexibility in optionally conveying auxiliary scalars and vectors. >>>>In Jmol, however, only integers are recognized (as formal charges), >>>>whereas Rasmol (and, I do believe Xmol) is fine with pretty much any >>>>float value. >>>> >>>> >>>> >>>> >>>PS: Hmm, I have access to a system still capable of running >>>Xmol-1.3.1 ;-) >>> >>> $Header: /g/src/prod/xmol/src/clients/xmol/RCS/xmol.c,v 2.0 >>>1993/05/11 16:43:28 jc Exp $ >>> >>>Still, I did some data archaeology and found already on the net: >>> >>> >>>XYZ(5MSC) man page: >>> >>> http://www.ccl.net/chemistry/resources/messages/1996/10/21.005-dir/index.html >>> >>>Sample file with fractional charges: >>> http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz >>> (This gets installed in the XMol distribution as: /usr/local/lib/ >>>xmol/examples/reacpth.xyz ) >>> >>> >>>G94-to-XYZ converter in C: >>> >>> http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c >>> >>> The format in the output loop is: >>> fprintf(stdout, "%s\t%f %f %f %f\n", ap->type, ap->x, ap->y, ap->z, >>>ap->charge); >>> >>> >>>Regards, Michael >>> >>>------------------------------------------------------------------------- >>>Check out the new SourceForge.net Marketplace. >>>It's the best place to buy or sell services for >>>just about anything Open Source. >>>http://sourceforge.net/services/buy/index.php >>>_______________________________________________ >>>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 >> >> >> >>------------------------------------------------------------------------- >>Check out the new SourceForge.net Marketplace. >>It's the best place to buy or sell services for >>just about anything Open Source. >>http://sourceforge.net/services/buy/index.php >>_______________________________________________ >>Jmol-developers mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > >------------------------------------------------------------------------- >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services for >just about anything Open Source. >http://sourceforge.net/services/buy/index.php >_______________________________________________ >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 ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
