P.J. Carroll wrote:
> I'm trying to compose a general web page that would allow
>users to construct a unit cell packing diagram using a CIF and
>whatever strategy they would like to pursue. My first attempt is at:
>
> http://macxray.chem.upenn.edu/cells/3159SG.html
>
>To develop this, tho, two changes would be nice:
>
>(1) right now, a symop, for example, -X, 1/2+Y, 1/2-Z, that would put
>a molecule in a neighboring unit cell with a negative X-coordinate is
>adjusted by Jmol so the co-ordinates are all positive. I would prefer
>that the symop -X, 1/2+Y, 1/2-Z actually put the molecule at a
>negative X! This is important if I have an external program that
>tells me there is a hydrogen bond between symop X, Y, Z and symop -X,
>1/2+Y, 1/2-Z. I would like to be able to draw those specific
>molecules with Jmol.
>
>
>
This sounds like a settable flag. something like
set jonesFaithfulAbsolute
I think that could be done.
>(2) could the command load "" {3 3 3} be changed to also accommodate
>negative co-ordinates? That is instead of loading cells 555 thru 777
>with 555 being the base cell, it would be nice if it loaded cells 444
>thru 666 with 555 being the base cell. Again, this change would make
>Jmol agreeable with other output that has, e.g., a hydrogen bond to a
>molecule at -1+X, 1/2-Y, 1/2+Z.
>
>
>
Here's the problem: {3 3 3} is short hand for "everything between
fractional coordinate {0 0 0} and fractional coordinate {3 3 3}." I
don't think there is anything really preventing us from using negative
coordinates, but "{-3 -3 -3" is probably not what you want. Maybe we
need a keyword such as
load myfile.cif cellRange 444-666
That might work. Because that could be coded as {444, 666, 0} and
intepreted as you wish.
I'll think about that.
>And finally that page referenced above was written for space group
>P2(1)/c and those four specific symops. Is it possible to communicate
>from the CIF the number of symops and their x, y, z expressions so a
>general page could be written that does not know the symops
>beforehand? Is this something that can be done by javascript?
>
>
>
ah, this is precisely what "jmolGetProperty" is for.
In JavaScript:
var Operators =
jmolGetPropertyAsArray("auxiliaryInfo").models[0].symmetryOperations
operator1 = Operators[0]
operator2 = Operators[1]
etc.
that "models[0]" assumes we are talking about the first model in the
file, which may contain more than one model, of course.
>Pat Carroll
>Chem Dept
>U of Penn
>
>
>
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