Thanks everyone. Angel I like your solution. I was not aware of amino.
In the code for FirstGlance, I enumerate all 20
amino acid names in order to select protein atoms
that lack alpha carbons. amino is much easier!
Does
select amino
fail to select something selected by
select protein
??
Thanks everyone. Angel I like your solution.
I thought so. It's more logical and general.
Why do we need both protein or amino?
amino is rasmol-compatible. protein is Jmol chemical intelligence,
particularly to account for funny cases like yours. Also, I think, it
includes
protein selects for groups that have been identified as amino acids. This
is done structurally rather than by some sort of name assignment. Since you
can have proteins that have all sorts of nonstandard amino acids, if you
really want ALL the amino acids, you should use
protein or amino
amino by
Dear Bob,
Each of the 4 chains in 1hjx ends with a residue, Thr383, for which
only a single atom, the main chain nitrogen, has coordinates. Jmol
(including 12.0.31) fails to recognize this atom as protein, despite
it being within group THR.
restrict not (protein, nucleic, hetero)
should
Part of the problem there may be that, as far as I understand, Jmol
algorithm for protein is more complex than identifying amino acid
residues by name (that's what amino does).
I think I read about the algorithm inside the source of
JmolConstants.java
I do not mean to defend that every atom
Years ago Jmol did not have a way of adapting to bizarre structures as well
as it does today, and the PDB database was littered with bizarre structures.
It's not a bug; Jmol requires an alpha carbon, not a nitrogen to define a
protein.
If you can find a number of additional structures in the PDB
chiming in from the sidelines: I agree with Bob... The bug here is that
PDB structure!
-Tom
On Thu, Feb 10, 2011 at 10:14 AM, Robert Hanson hans...@stolaf.edu wrote:
Years ago Jmol did not have a way of adapting to bizarre structures as well
as it does today, and the PDB database was littered
Maybe this:
select amino and not protein # will pick those anomalous atoms
select protein,amino # will pick all protein atoms
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