Dear Yang Li:
Happy New Year to you, too, (ahead of Feb. 7th).
You certainly owe us no apology; the reverse may not be true.
Your question is an important one, as is what you have written below.
I'm not certain I have a completely satisfactory answer.
The reason is that ideal bond lengths may or may not be true in the
sense that the value is established by social consensus, and is thus
guaranteed to be perfectly accurate, even though it may be quite precise.
Because of this, and because of natural deviations from ideality (which
really only become trustworthy observations at extremely high resolution),
a certain amount of wiggle room is typically allowed in terms of rmsd.
The more conservative the refinement, the smaller the rmsd from ideality
will be.
Some people believe 0.02 Å deviation from ideality is reasonable, based on
the accuracy of the dictionary values of bond lengths and angles; others
consider that to be too sloppy and a way to artificially deflate
Rfactors.
I seem to have detected a tendency in the literature to aim for about 0.01
Å deviation. The new refinement program phenix.refine, which is supposed
to optimize weighting between X-ray terms and stereochemical constraints
automatically, seems to settle in at quite conservative values, such as
0.005 Å, whereas with refmac, I can't seem to get the geometry any more
ideal than 0.005 Å even if I try to idealize a structure in the absence of
X-ray data.
So, like you, I am a bit confused, and wouldn't mind hearing more from the
experts.
All the best,
Bill
yang li wrote:
Dear All,
I am very sorry to involve you into such insignificance discussion,
I
have reached agreement
with Prof Gerard, please stop talking about things beyond science, thanks!
I read a book today, which said A refined model should exhibit rms
deviations of no more
than 0.02A for bond length and 4 for bond angels, I just wonder about the
standard of the
bond length and the bond angel. I think most of you have read similar
words!
But maybe I
didnot express clearly and made some phrasal mistakes.
At last, happy new year to you all--though very late!
Sincerely!
Yang Li
