On May 31, 2006, at 11:32 a, Angel Herraez wrote:
(Jmol 10.00 and 10.2)
On a DNA, hydrogen atoms in pentose are selected with 'sidechain',
not with 'backbone' as I expected (from Rasmol/Chime).
if I recall correctly (I can not test), Chime had trouble with
nucleic backbone hydrogens as well. I thought we addressed this
issue when we defined nucleic but obviously not. my apologies.
one kludge is to use the within command, which is what I used to do
with Chime:
select (nucleic and (backbone,(hydrogen and within(1.9,backbone)))
I guess this is intentional (I recall a similar finding with glycine
H atoms on Calpha), but find no use for it, and it makes difficult to
select parts of the molecule.
E.g., "select sidechain; spacefill on" will spacefill H atoms in the
backbone
and there is no way to distinguish pentose H atoms from base H atoms
while, in my proposed implementation, it would be easy --if just
strict backbone was intended-- to select "backbone and not hydrogen",
or "backbone and hydrogen", "sidechain and hydrogen", "bases and
hydrogen", etc.
I agree that Jmol should be able to distinguish backbone from non-
backbone hydrogens, without resorting to work-arounds like the one
above.
I would hence vote for assigning H atoms to backbone set when they
are bound to backbone C, N, O atoms.
Opinions?
so this is also a problem with the protein set as well? I'll have to
go back and see what we did here.
tim
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