Dean Johnston wrote:
>>I have just checked in a version of Jmol that allows:
>>inverting selected atoms about points and planes
>>
>>
> I like it! I thought about asking to add something like this a while
>back, but never got around to submitting an official feature request. I can
>think of some really nice ways of using this capability. (I'm working on
>some pages that illustrate concepts of point-group symmetry - see
>http://www.otterbein.edu/home/fac/dnhjhns/xmltest/demo.html ) I still
>haven't had time to digest the cool new scripting capabilities...
>
>
>
great -- you can use the Miller indices and select symmetry operation sets:
select symop=1555
invertselected HKL {1/2 1/2 0}
oooh.
>>And, yes, I know -- the next thing needed is "rotateSelected". I'm
>>working on that.
>>
>>
done - that works, too.
> Any chance you can think about improper rotations as well? :-)
>
>
>
Let's see.. What's an improper rotation again? Oh, sure, that's trivial --
angle = 60
rotate internal @angle {....} {....};
select *;invertSelected POINT {...};
Right?
>>Comments? Suggestions for perhaps a SIMPLE general format for writing
>>coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited,
>>but with bonds), PDB? (unlimited, but rather involved).
>>
>>Alternatively, should Jmol have a new "native format" that includes the
>>"state"?
>>
>>
> If Jmol is creating it, what you have looks ok (except for connectivity).
>I don't know if bonds should be stored like MOL files or as Jmol commands
>(like the state). I like the idea (in principle) of using XML, though it
>certainly doesn't fit the "simple" criterion.
>
>
>
It's really not important. If you
write coord state.spt
and then
load state.spt
the nice thing is that it's all one file now. But you are pretty much
just back to what you get in an XYZ file.
But if you instead have that original file still in place and
script state.spt
then it loads the original file and moves the atoms to where they need
to be.
Bob
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