Bob Hanson wrote:
...
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)
This is answered by Angle Herraez, I wanted to point your attention to
the existing RasMol2.7-molecule concept.
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)
No, only in the case of the large PDB files where the Jmol model concept
is violated.
(Up to now, I've not played with Jmol crystals, but for sure it is very
interesting to determine crystal contact sites, which is possible with
your nice applet but Mouse picking distances generate strange line parts.)
? 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.
within(covalent, selection)
# I vote for "covalent", if covalent is the criteria (backbone,
SS-bonds, chemical cross linker) to avoid confusions with RasMol2.7
"molecule"?
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
color atoms covalent
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
very nice.
Regards, Jan
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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