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.




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