Patrick J. Carroll wrote:
>Bob,
> I'm trying to work through your suggestions about using "display",
>but meanwhile, I've noticed some other strange behavior. On that same page,
>
> http://macxray.chem.upenn.edu/gam/9129b.html
>
>when I try to add a molecule by using symmetry operation no. 3 (center of
>symmetry), when I try to select symop = 3555, the green Ni atom in symop =
>1555 is instead selected. This is the atom that lies on the symmetry
>element (at .5, .5,.5).
>
That Ni atom is in both 1555 and 3555. Everything on that page looks to
me to be working right after a "fill cell" operation.
fill cell, then...
console
selectionHalos on
select symop=1555 # looks right
select symop=3555 # looks right
select symop=1555 and symop=3555 # just that Ni atom
I think 3555 is not working properly, but not for the reasons you think.
That Ni should be present, but the other selected atoms should also be
in cell 555, and they are not.
Is that the problem, perhaps? If so, I'll look into that. I think it
probably has something to do with how the symmetry gets defined using
load cifs/9129.cif {444 666 0}
I think what's happening is that 3555 for atoms other than the base set
is getting shifted over by one unit cell and really pulling in 3444.
Yes, that's it.
select symop=3666
gets you what you expect for symop=3555, I think, from that load.
So I will fix that.
Thanks.
Bob
Bob
>I have seen this behavior in other cells whenever
>an atom lies directly on a symmetry operation and I select a symop that
>should be the symmetry-related molecule, the atoms in the central molecule
>(1555) that lie directly on the symmetry element are selected, instead.
>See, for example
>
> http://macxray.chem.upenn.edu/lgs/3160b.html
>
>In this case, several of the atoms in 1555 lie on a mirror plane at y=.25.
>When I try to select symop = 4555, these atoms in 1555 that lie on the
>mirror plane are selected instead.
>
>
>
>Pat Carroll
>UPenn X-ray Facility
>
>
>
>
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