Dan Gezelter wrote:
>
>>1) Are ORTEP anisotropy parameters just three scalars that are
>>Cartesion x,y,z-based?
>>
>>
>
>Umm... I'll answer with a qualified "yes", but getting those out of the
>ORTEP-style input files is sometimes a challenge. If you want a
>scary look
>at the most archaic way of getting data into a program, look here:
>
> http://www.ornl.gov/sci/ortep/doc/input.html#temp
>
>
>
lovely. If you like that, check out AWOS automated weather observation
report format:
http://www.msc-smc.ec.gc.ca/msb/manuals/awos/appxa_e.html#appxa1_e
>The thermal ellipsoid is specified with an upper triangular matrix:
>b11, b22, b33, b12, b13, b23, but the basis set for this matrix may
>be the crystal axes.
>
>
>
The important thing for me is what is in the CIF file, I think. or SHELX.
EU1 5 0.815442 0.194311 0.684236 11.00000 0.02058
0.02154
0.02062 0.00063 0.00191 0.00089
ah, I see from http://msg.ucsf.edu/local/programs/shelxl/ch_07.html#MERG
that those last six numbers are your upper triangular matrix.
OK, what is this matrix telling me?
>>2) Same question for your work.
>>
>>
>
>We've got uniaxial ellipsoids (a = b != c) , so a single vector is
>enough to specify
>the orientation of the c axis. Also, we've been packing the extra
>data on the
>eccentricity into the extended columns in the XYZ file format:
>
>atype x y z ecc cx cy cz
>
>
oooh, so that's trivial. Just align with the vector, contract, and go.
How about just:
isosurface center {x y z} eccentricity {cx cy cz ecc} ellipsoid
or
isosurface center {x y z} ellipsoid {cx cy cz ecc}
?
>Here, cx, cy, and cz specify the orientation of the "c" axis of the
>ellipsoid,
>and ecc is the length-to-breadth ratio (c/a). We can easily clone
>the XyzReader
>to make something more general that would specify two of the three axes:
>
>atype x y z a b c ax ay az bx by bz
>
>(or we could even specify all three, but we'd need to check for
>orthogonality
>of the vectors.)
>
>
I recommend switching to upper triangular matrix notation :)_
>To answer Miguel's questions:
>
>
>
>>>>Q: Do people want to render proteins with thousands of
>>>>ellipsoids? Or is
>>>>this generally applied to smaller molecules (or small portions of
>>>>proteins)?
>>>>
>>>>
>
>Most ORTEP renderings are for smaller molecules (probably at most a
>hundred
>or so thermal ellipsoids). We're rendering liquid crystalline
>simulations
>with a few thousand ellipsoids (and a few thousand frames of the
>simulation),
>but we typically use atoms / vectors to find an orientation we like
>and then
>export to pov ray.
>
>
>
>>>>Q: Are all the ellipsoids the same shape, just scaled to
>>>>different sizes?
>>>>Or are some of them more elongated than others?
>>>>
>>>>
>
>In ORTEP, each atom has a different ellipsoid (with different
>eccentricities).
>
>In our stuff, there's a limited number of possible ellipsoidal
>geometries.
>
>
>
>>>>Q: Within a given molecule, are there usually multiple ellipsoids
>>>>that are
>>>>the same size & shape?
>>>>
>>>>
>
>In ORTEP? No.
>
Actually, I see there is provision of this:
If U is given as -T, where T is in the range 0.5 < T < 5, it is fixed at
T times the U_eq of the previous atom not constrained in this way. The
resulting value is not refined independently but is updated after every
least-squares cycle.
not that I have a clue what that says!
> In our stuff? Sometimes.
>
> --Dan
>
>
>
Bob
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