So let's say I am back in the good old days before computers, hand-calculating the MIR phase of my first reflection--would I just set that phase to zero, and go from there, i.e. that wave will define/emanate from the origin? And why should I choose f000 over f010 or whatever else? Since I have no access to f000 experimentally, isn't it strange to define its phase as 0 rather than some other reflection?
JPK On Wed, Oct 13, 2010 at 7:27 PM, Lijun Liu <lijun....@ucsf.edu> wrote: > 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" <wgsc...@chemistry.ucsc.edu> > To: <CCP4BB@JISCMAIL.AC.UK> > 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: j-kell...@northwestern.edu > ******************************************* > > Lijun Liu > Cardiovascular Research Institute > University of California, San Francisco > 1700 4th Street, Box 2532 > San Francisco, CA 94158 > Phone: (415)514-2836 > > >
