[EMAIL PROTECTED] 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
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