Re: [Jmol-users] Selection problem with structure 1TON

[Jan R. <jo...@gm...>]

rh...@fl... wrote:
>     Hi all,
>
> Jmol 10.00.33 and 10.00.18 seem to be unable to select any protein residue range
> in  the PDB structure "1TON" from the PDB database (e.g.: 53-58). In contrast
> version 10.00.00 is able to do this.
>
> When I looked at the PDB file I noticed that it contains no chain identifier and
> that the "HOH" residue numbering starts at 1, overlapping with the protein
> residue numbering. It looks like this could cause the problem. With "113I", a
> similar structure without this kind of overlap, Jmol 10.00.33 doesn't show any
> selection problems.
>
> I don't know if "1TON" is still within the PDB format specifications and how
> many other PDB structures also have this kind of overlap. So maybe this isn't a
> bug but just a reduced error tolerance.
>   
That is what PDB format guide tells us:
"
* Chemical modifications of standard residue side chains by addition of
new atoms are handled as follows:

    - The new atoms are represented as a HET group. This group is
assigned the chain name, sequence number, and insertion code of the
standard residue that it modifies.
"

without a chainID for its one, the HOH groups seamed to be modifiers of 
the corresponding residues.

but "Modified standard residues must have a corresponding MODRES record"
which is absent, in any case it is

a Jmol problem, why didn't Jmol select all residues 53-58, in fact
Jmol select only the HOH residues (modifying groups or not) and overlook 
the standard amino acids.
Regards, Jan