Dear Bob,

> questions answered in line below...

Sorry for the delay; I looked back in the R.E.D. code.

> Jmol doesn't need atom symbols, but as you can imagine, CA for calcium and
> CA for alpha carbon is not conducive to unambiguous resolution of elements
> without that key field. There are no rules about atom names having to start
> with element symbols, so Jmol can only apply a reasonable guess algorithm to
> get elements when that element field data is missing.

Yes, you are right...

> - Many small molecules are written in the PDB file format without
>> these chemical elements
>
> Yes, but for them the atom name "CA1" is interpreted as calcium, as you
> would expect. Same for Ce1, Cd1, Cf1. How could Jmol be expected to read
> those as carbons?

In fact, R.E.D. deals only with chemical elements up to Bromine; this  
means there is only one ambiguity in our case; CA for calcium versus  
CA for alpha carbon.

>> - VMD and LEaP (for instance) do not need chemical elements to
>> recognize atom names
>
> And they will make the same mistake -- or not recognize cerium as a possible
> atom. VMD has all sorts of known problems figuring out elements from atom
> names.

ok, as we work in the field of organic & bio-organic molecules we do  
not encounter these problems, I see.

> Jmol does this already. but you can't throw generic "PDB-like" files at it
> and expect it to know that CA1 means alpha carbon and not calcium. One could
> suggest that ATOM requires CA be alpha carbon and HETATM might not, but it
> turns out that's not workable, either.

ok

> Jmol recognizes that if you start "CA1" in column 13, then you must mean
> calcium, and if you start it in column 14, you mean alpha carbon. That is,
> columns 12 and 13 indicate atom symbol. So that's an option. (The atom names
> are spit out by many programs in this way -- all the RCSB PDB files are like
> this, for example, even if it is not in the specs.) This system breaks down
> for certain hydrogen atoms that are named as, for example, "HH11" or "HO5'".
> For "HO5'" Jmol checks to see if this is a HETATM (so this is read as
> holmium, or ATOM (so this is read as hydrogen). Obviously the best situation
> is to create proper PDB files and have that colum 77/78 data.
>
>> Consequently, this means that Jmol can already recognize some atom
>> names without chemical elements. Is it not possible to extend this
>> feature to more general atom names?
>
> Right, that's because Jmol has a fallback option. The rule is that the atom
> symbol should appear right-justified in
> columns 13 and 14. But if that's not the case, as here, then the algorithm
> looks next at just the character in column 13. In this case C and H.
>
> By the way, are you sure ATOM is appropriate for a benzene ring? According
> to the specs we have:
>
> The ATOM records present the atomic coordinates for standard residues (see
> http://deposit.pdb.org/public-component-erf.cif).
>
> Everything else should be HETATM. The only difference that makes for Jmol is
> for four-letter
> atom names that are therefore forced to start in column 13, start with H,
> but aren't hydrogen. Like,
> for example, HE for helium or "hydrogen E". In that case, if it is HETATM,
> Jmol chooses helium; if it is ATOM, it chooses H.

ok

Thanks for all these explanations. all makes perfect sense. I have  
modified R.E.D. IV so that the PDB format generated always contains  
chemical elements so that Jmol does what we want.

regards, Francois



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