Bob Hanson wrote:
...
b) What WOULD you use if you had it available?
the monitor/measure command, especially if there is no need for atom
numbers but select expressions could be used
Hmm. Usually for those you need an ordered list, right? But one could
imagine following the bonding in some cases.
Say more.
I don't see a difference whether I say
monitor 2087 2088
or
monitor ([LIP]3:A.O5) ([LIP]3:A.O6)
( is signaling that a select expression has to be evaluated first to get
the monitor command argument
the show selected command to evaluate current selection
done check out
http://www.stolaf.edu/people/hansonr/jmol/test/json/json.htm
c) What sort of information (exactly) are you looking for?
depends on the status of set picking, in most cases
set picking atom
show orientation
show center
RasMol>show selected group
RasMol>set picking distance
these are taken care of by getProperty(). -- no need for callbacks here.
OK with that
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.
d) Is there a particular format that you would like to see,
other than just the current text-stream of messages?
I like the ready to use command line like output, e.g.
picking should result in a ready to use select expression
[LYS]54.CD #798
is OK, it isn't difficult to filter e.g. [LYS]54.CD from this.
so, for example:
msg: 58,atomPick,296,[ASP]43.O #297
msg: 57,atomPick,223,[CYS]32.N #224
msg: 56,atomPick,222,[GLY]31.O #223
msg: 55,atomPick,226,[CYS]32.O #227
right?
as I wrote, I like atomInfo[n].info
$ show orientation
moveto 1 -1000 0 0 180.0;
OR
reset; rotate z 180.0; rotate y 180.0;
no problem.
getProperty("orientationInfo")
orientationInfo=new Array()
orientationInfo.moveTo="moveto 1 -791 -611 24 78.4;"
orientationInfo.rotateZYZ="reset; rotate z -126.6; rotate y 78.3;
rotate z 128.8;"
orientationInfo.rotateXYZ="reset; rotate x -75.6; rotate y -35.7;
rotate z 30.2;"
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>
Regards, Jan
...
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