Hi Tom This all dates back to compatibility with Rasmol and Chime scripts. Rasmol was designed to be used mostly with pdb files, and Jmol 10 wanted to inherit that functionality (which is just wonderful for us biochemists ;-) ).
So, these are Rasmol tokens that shouldn't change, but I think that at the current state of Jmol they can certainly be hidden from the users, which will not in general be familiar with them. > Also, I've never understood the difference between "Ligand" and "non- > solvent hetero" - are they not redundant? Yes, they are exactly the same. "ligand" generally means ligands, but is not always identical to what one would expect. It is defined strictly as "hetero and not solvent" Of course, "hetero" only applies to pdb-format files and related ones like mmCIF, where it is strictly defined as the set of atoms having an HETATM key rather than an ATOM key. I'm not sure now what Jmol does with non-pdb files (for which "protein" and "nucleic" sets are defined independent on the standard PDB names for amino acids and nucleotides), but I think there is just no "hetero" in those. You could do "not protein and not nucleic" I guess. (Oh, all this is needing a more detailed discussion. Maybe a page in the Wiki. Aha, for pdb formatted files the discussion is already written, in my book, pages 59-60 ;-D ) Anyway, > Finally, I think the context specific use of "HETATM" and "hetero" is > confusing to those unfamiliar with the PDB syntax/nomenclature. I'd > like to see just "ligand" and "solvent", although an argument could > also be made for including "ions"... Again, we are quite stuck with the traditional terms. Indeed, there IS an "ions" term, defined as "solvent and not water". Not really useful, since e.g. calcium ions will not go there. Particularly, "ions" in PDB are just phosphate and sulphate --and that's the only difference between "water" and "solvent". It makes sense in crystallography, but does cover all nonaqueous solvents found in the PDB. > Is there a better word for "non- > water & non-protein & non-nucleic acid"? :} That's a good idea, but as long as it will only apply to pdb files it would be misleading. > Lastly, is there a > strong need to parse water and non-aqueous solvents in the sub-menu? See my comments above. Not too important really. There are very few phosphates and sulphates. All this makes me think that we could devise a menu that works similarly for pdb and non- pdb files, with a common, non-pdb-specific terminology. --Another hit for Jmol 12-- I'll give it a thought and come back with a proposal. ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users