[Jmol-users] amino acids not classified as protein

[Rolf H. <rh...@fl...>]

      Hi all,

among others there are the following predefined residue sets available
in Jmol: "amino" and "protein".

The documentation at "http://chemapps.stolaf.edu/jmol/docs/" states that
  "amino" is defined as "all twenty standard amino acids, plus ASX, GLX,
UNK".

For "protein" it states as definition "defined as a group that contains
PDB atom designations C, N, and CA".
A few weeks ago Bob explained that there is an additional condition for
"protein": contains PDB atom designations O or O1.
And if all residues contain only CA atoms they are also put into the
"protein" set (e.g.: 1A1D).

This means that the "amino" set is restricted to standard amino acid
residues while the "protein" set also includes modified amino acid residues.

But there are for example PDB entries where only C,N and CA atoms are
present for standard amino acid residues (e.g.: 1L9U). These are put
into the "amino" set but not into the "protein" set.

Q: Why are residues that are recognized by their name as standard amino
acid residues not also put into the "protein" set irrespective of the
atoms that are available?

If a standard amino acid residue only contains C,N and CA atoms there is
 no "trace" or "cartoon" drawn. In the case of "1L9U" nothing is drawn
at all. In other cases where only some residues don't have oxygens the
"trace" and "cartoon" is disrupted.

Q: Is the missing cartoon/trace a consequence of the missing
classification as protein or are there other reasons?

---- Test System ----------------
 Jmol: 11.3.47, application
 Java: 1.4.2_13
 OS  : Linux, SuSE Enterprise 10
---------------------------------

Regards,
Rolf