At 08:00 on 18 November, Miguel wrote: > Anthony wrote: > > > I have been using JMol to display xyz files, and I have found that > > deuterium (element "D") is set to have a much larger covalent radius > > than H. > > Hmmm ... but there is no special support for deuterium ... so it must be > being treated as "unknown" > > Q: Are they very large and colored 'hot pink' ?
Yes, they are. > If you say 'label %a' I suspect that these will be tagged as element 'Xx'. > > > Presumably I could correct this using a script, but I would > > rather correct the default value. > > In this case, we need to figure out what the correct treatment should be. > > > However there doesn't seem to be any > > accessible table of default values, or any way to change them from the > > JMol program. > > You are correct. The table is compiled into Jmol. > > > Have I missed something? I would like to see the default > > values (radii, colours and any other property) tabulated in an ASCII > > text file that is read in by the program. Then the default values > > could be changed easily without any need to incorporate code for doing > > it into JMol. > > Others have asked for the same thing. It is a good feature to implement > after the official v10 release. > > In the meantime, tell me some more about 'deuterium'. > > Q: Is 'D' the accepted element symbol. D is commonly used as the atom symbol for deuterium when it's necessary to distinguish it from the common H isotope. > Q: What other elements have common 'alternate elements' for isotopes? None, I think, but it is sometimes necessary to distinguish between atoms of the same element that are different in some way -- for example C in methyl groups as distinct from C in carbonyl -- or conversely to recognise that atoms labelled differently for one reason or another in an xyz file are actually the same. In the case I described, I would have been content for D to have been recognised as an alias for H and treated accordingly. > Implementing support for isotopes like this may not be straightforward. I don't think a general treatment is the answer. This is why I advocate the use of a separate file of atom properties that can be modified to suit individual requirements. It would be necessary to allow additional entries -- not just one for each element -- to provide for aliasing, so that, for example, H and D could be separate entries, with the same properties or different ones depending on the circumstances. Support within the program for editing the property table would be nice but not essential. -- Anthony Stone http://www-stone.ch.cam.ac.uk/ University Chemical Laboratory, Email: [EMAIL PROTECTED] Lensfield Road, Phone: +44 1223 336375 Cambridge CB2 1EW Fax: +44 1223 336362 ------------------------------------------------------- This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS DOWNLOAD - A multidimensional database that combines robust object and relational technologies, making it a perfect match for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8 _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
