Bob Hanson wrote:
right, that's my point. It seems unnatural to me as well. That's why I
was surprised and initially thought it was a bug. Personally I can't
imagine it, either, unless....
...I suppose some day we will be loading two molecules and maneuvering
them independently (like a drug and an active site). In that case they
will (probably) be in two different frames because they will have been
loaded from two different files, and the interesting thing might be to
highlight what atoms in one molecule are near atoms in another.
So maybe someday there will be a flag that can be set -- only within a
model, only between models -- still I find it hard to believe one
would ever want the current "within or between models".
I have a feeling that the logic would get totally unrulely if we tried
to restrict "within" to a particular model. Because this has to result
in a linear set of bits.
The implementation is probably really very simple, with one line
modification.
In Eval.withinDistance(), replacing:
AtomIterator iterWithin = frame.getWithinAnyModelIterator(atom, distance);
by
AtomIterator iterWithin = frame.getWithinModelIterator(atom, distance);
Nico
Bob
Nicolas Vervelle wrote:
Angel Herraez wrote:
Diificult to distinguish, since most atoms nr. 3 are close to each
other.
I have tested with another file and yes, it is selecting atoms in
any model that are close to specified atom in any model (i.e, not
only within the same model).
Test attached PDB file using atomno=22 as the reference
From my totally non-expert point of view, this behavior seems very
strange and unnatural.
(since different models could be totally unrelated to each other, or
related in different ways)
I don't see why someone would want to select atoms at coordinates
near at atom in an other model.
But you are the experts, not me ;)
· · · · · · · · · · · · · · · · · · · · · · · · · · · · ·
Dr. Angel Herraez
Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
E-28871 Alcala de Henares (Madrid), Spain
fax: +34-91 885 45 85
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