[Ifeffit] P 1 space group

[Anatoly Frenkel]

Hi Scott,

For molecular substances, the accuracy in atomic coordinates that are
obtained by one of the three most popular methods (e.g., in Protein Data
Bank, the sources are X-ray crystallography, solution NMR, or theoretical
modeling, here is a good review:
http://www.rcsb.org/pdb/experimental_methods.html) is much worse than 0.1 A.
I got this number assuming the resolution of 1 A (considered high for a
protein, see the link above, and estimating the uncertainty of the position
of an atom as roughly one tenth of the resolution, again using the quote
from the same article. Thus, in such protein, x-ray crystallography would
not guarantee atomic positions with better than 0.1 A accuracy.

Resolution provided by solution NMR is "not as detailed and accurate as that
obtained crystallographically" - the quote from the same source.

Therefore, for all purposes, creating a pseudo cubic cell will halp: choose
lattice parameters 99.9, 100 and 100.1. This will introduce 0.1% error in
the distances that are obtained by Atoms for such P1 unit cell compared to
those obtained by Atoms for a cubic cell. This 0.1% error in distances is
negligible for all purposes.

I am not sure Atoms will allow the lattice parameters to be that close but I
do not see why it should not.

Anatoly

-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov]On Behalf Of
scalvin at slc.edu
Sent: Sunday, October 02, 2005 11:32 AM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] P 1 space group


Hi Bruce and others,

Back in the day, I used to use a "trick" for generating feff files for
non-crystalline, molecular substances (or small nanoclusters). I'd use a
space group of P 1 with a = b = c = 100, and alpha = beta = gamma =
90...then I could enter coordinates in hundredths of an Angstrom.

But I tried the trick recently, and the Atoms inside Artemis complains
that I should be using a cubic space group and doesn't run.

I don't know my space groups very well, but is there actually a cubic
group that doesn't have any symmetry within the unit cell? It seems to me
that a real material (not just my trick) could have an "accidentally"
cubic unit cell without being a cubic space group. Can someone who knows
crystallography better than I do confirm that?

If so, then atoms could issue a warning, but should not prevent a feff.inp
file from being generated.

Incidentally, of course I know there's a fairly trivial alternative to my
trick...I could just create the feff.inp file without using atoms (Artemis
even conveniently provides a template). But I think it's marginally easier
for some of those new to the software to use the P 1 method, because then
they don't have to think about potential lists and such.

--Scott Calvin
Sarah Lawrence College

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