Jan wrote:
Bob Hanson wrote:
Is this a "feature" or a "bug"? Should "within" restrict itself to a
given model, or is it interesting or important that one be able to
select "within" a distance across multiple model sets?
it is an important *feature* that one is able to use within across
multiple model sets.
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.
this case is called "molecule" in RasMol2.7. and I don't want to load
them as two separate PDB-MODELs in Jmol "animation frames". They could
be addressed for maneuvering independently but should be in the same
MODEL allowing measurements between molecules.
Jan, I wonder if you are confusing "model" and "molecule" perhaps? Your
last statement there -- that you do NOT want to load them as two
separate models suggests that you do NOT think that "it is an important
feature to be able to use within across multiple models in
multiple-model sets. Am I right that you are interested in this
specifically across MOLECULES within the same model?
model set -- a set of frames, one model per frame
molecule -- as set of covalently bonded atoms, perhaps one per frame,
but usually (as in crystals) one or more per model (per frame)
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.
This is easy
select within(4.2, atomno=3 AND */1) AND */1
Right. Can you give an example of where you would want those */1 out? In
other words:
select within(4.2, atomno=3)
? Question is whether you see a use for cross-MODEL within. (I think I
do, but my point is simply that it shouldn't the the default.)
By the way, in the prototype I have added "within molecule" (not model
-- real, covalent set molecules) and will be expanding on this.
select within(molecule, atomno=35)
#all atoms of molecule containing atomno=35 (in all frames)
select within(4.2, within(molecule, atomno=35)) and not within(molecule,
atomno=35)
#all atoms in nearby molecules
color atoms molecule
#color from red to blue in molecule 1,2,3,..... by molecule
As a bonus, this calculates the molecular formula of the molecule. But I
don't think I have that displayable yet.
I need "moleculeinfo" I think.
You can see this at work at http://fusion.stolaf.edu/chemistry/jmol/xtalx
Clicking the radio buttons should do some interesting molecule-based
selections. You can see what those buttons are doing by using
http://fusion.stolaf.edu/chemistry/jmol/xtalx/?NOAPPLET
highlight "first molecule"
select *; color atoms cpk;select within(molecule,atomno=1);color blue
highlight "by molecule"
select *; color atoms molecule
Bob
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