When talking about the reflection phase:
While we are on embarrassingly simple questions, I have wondered for
a long
time what is the reference phase for reflections? I.e. a given phase
of say
45deg is 45deg relative to what?
=========
Relative to a defined 0.
Is it the centrosymmetric phases?
=====
Yes. It is that of F(000).
Or a theoretical wave from the origin?
=====
No, it is a real one, detectable but not measurable.
Lijun
Jacob Keller
----- Original Message -----
From: "William Scott" <[email protected]>
To: <[email protected]>
Sent: Wednesday, October 13, 2010 3:58 PM
Subject: [ccp4bb] Summary : [ccp4bb] embarrassingly simple MAD phasing
question
Thanks for the overwhelming response. I think I probably didn't
phrase the
question quite right, but I pieced together an answer to the
question I
wanted to ask, which hopefully is right.
On Oct 13, 2010, at 1:14 PM, SHEPARD William wrote:
It is very simple, the structure factor for the anomalous scatterer
is
FA = FN + F'A + iF"A (vector addition)
The vector F"A is by definition always +i (90 degrees anti-
clockwise) with
respect to the vector FN (normal scattering), and it represents the
phase
lag in the scattered wave.
So I guess I should have started by saying I knew f'' was imaginary,
the
absorption term, and always needs to be 90 degrees in phase ahead of
the f'
(dispersive component).
So here is what I think the answer to my question is, if I understood
everyone correctly:
Starting with what everyone I guess thought I was asking,
FA = FN + F'A + iF"A (vector addition)
for an absorbing atom at the origin, FN (the standard atomic
scattering
factor component) is purely real, and the f' dispersive term is
purely real,
and the f" absorption term is purely imaginary (and 90 degrees ahead).
Displacement from the origin rotates the resultant vector FA in the
complex
plane. That implies each component in the vector summation is
rotated by
that same phase angle, since their magnitudes aren't changed from
displacement from the origin, and F" must still be perpendicular to
F'.
Hence the absorption term F" is no longer pointed in the imaginary
axis
direction.
Put slightly differently, the fundamental requirement is that the
positive
90 degree angle between f' and f" must always be maintained, but their
absolute orientations are only enforced for atoms at the origin.
Please correct me if this is wrong.
Also, since F" then has a projection upon the real axis, it now has
a real
component (and I guess this is also an explanation for why you don't
get
this with centrosymmetric structures).
Thanks again for everyone's help.
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax) =
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [email protected]
*******************************************
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836
