On Tue, April 4, 2006 1:34 pm, Bob Hanson said: >> >> >> Any symbol may be used as the "atom type" and that symbol (case >> included) >> is then forever associated with that atom type defined. So I don't think >> it is a good idea to assume you can change case to make comparisons or >> assignments. > > true, but in this case Jmol is comparing just to see if that atom type > symbol matches a known element symbol for the sole purposes of > identifying the element. Certainly it could make a mistake, but that > is the case now in ALL cases. If some author chooses to enter > > Copper > > in for that field, then it will be read as "cobalt". So that's not an > issue. If the field were being saved for other purposes, I think I'd > agree. The CIF specifications are completely open here, and as in so > many cases, Jmol has to make its best guess as to what the element is. > The atom Label field is what is being kept, not the atom type symbol > field, and that field stays all caps.
What is Jmol doing with the assumed element type? That has a major bearing on what level of effort needs to be applied. I use a multi-level approach: - read the _atom_type.symbol loop - if the .radius_bond and .radius_contact distances are defined in the loop then add these to the table for the given .symbol. - if they aren't defined then use the .scat (factors) to determine the element type and do a table lookup for default .radius_* values for that element. - if there are no scattering factors (no coefficients and no table) then make a guess based on the provided symbol [aside: it is actually kinda silly that the cif specs don't provide for an absolute element identifier in the atom_type family] Rich ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
