Jan wrote:
I don't see a difference whether I say
monitor 2087 2088
or
monitor ([LIP]3:A.O5) ([LIP]3:A.O6)
Oh, sure. OK. I don't know that we are headed that way wth the monitor
command, because there are some programming issues with putting two atom
expressions in the same command -- nothing really insurmountable,
really, but not exactly trivial.
I thought you were talking about, say, specifying four atoms and then
somehow Jmol was to decide what arrangement you wanted for a dihedral.
THAT seems prone to problems.
But I don't see why we couldn't have:
getProperty("getDistance", "[LIP]3:A.O5", "[LIP]3:A.O6")
Mostly I don't like special cases. So the challenge would be to make
this extensible to
getProperty("getAngle", "[LIP]3:A.O5","[LIP]3:A.O6","[LIP]3:A.O7")
getProperty("getTorsionAngle",
"[LIP]3:A.O5","[LIP]3:A.O6","[LIP]3:A.O7","[LIP]3:A.O8")
Anyway -- these would be in the category "not a callback," I think.
But it's a great idea, and one that we'll definitely implement somehow.
I'm assuming for this idea:
1) You don't want to (necessarily) display the monitor line w/ or w/o
numbers
2) You want to be able to display the monitor line w/ or w/o numbers (do
that separately, with a script command, but that command format could be
returned as one of the elements of the data structure).
3) All three -- getDistance, getAngle, getTorsionAngle -- should be
available. Maybe a simple "getPosition" as well, just to head off the
obvious request.
Yes, I could imagine this to be very useful.
By the way, Jmol caches up to 16 measurements. (Something the applet has
never
had an interface to.) That is, you can make up to 16 measurements by
clicking the
mouse, and they are all saved automatically. The Jmol application
utilizes this for its table; there's no reason not to expose it as a
JSON structure to the web page.
The distinction I think I want to make here is the .script() method used
solely/primarily for driving the display; the .getProperty() method for
retrieving information. We can talk about .setProperty() or
.scriptSynchronous() later....
callback would only be luxurious for Jmol console use and especially
with a console only mode, if a Jmol --nodisply batch run option would
get implemented like in RasMol, if the applet is used, JavaScript is
already involved and there is no need for callback via JmolScript,
getProperty() is superior, callback is only used for functional
compatibility with RasMol scripts.
callbacks don't have any relation to the console -- those are just
messages. The function of callbacks -- or their replacement with
getProperty("callbackStatus","...") -- is to deliver timely information
about user activity. When there is no user, there is no issue with
callbacks, I think.
RasMol>show selected group
should result in a select expression
Hmm. That's an interesting idea. How does it choose the "right"
select expression? But I see what you are
after -- so that you can save that and recall that particular
selection. This could be tricky....
The right is *a* short expression, if 16/16 atoms of a group are
selected, no doubt, no individual atom should be selected. There is no
need for the shortest, but a symbolic human readable expression is
preferred over *only* an ordered atom number list (needed for compare
operations).
e.g.
>=1 model? <model expression>
>=1 chain? <chain expression>
>=1 group? <group expression>
>0.5 group? <group expression> and not ( <atom expression> )
>4 atoms? <group expression> and ( <atom expression> )
backbone? <group expression> and backbone
: <atom expression>
This would be a major challenge, I think. But at least you can do
getProperty("atomInfo","(atom selection)"))
so if you like that, maybe that's all we need for now. At least with
that you get the individual atom list.
Bob
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