This is all explained in the Wikipedia reference on refractive index I gave: http://en.wikipedia.org/wiki/Refractive_index#Dispersion_and_absorption . In the case that the material absorbs some of the radiation, the refractive index become complex: see the equation 5 lines from the beginning of the "Dispersion and absorption" section. The real part of the r.i. is the part whose variation with wavelength is the dispersion and so is the "dispersion component", and the imaginary part is the "absorption component". Dispersion and scattering are of course related since they both arise from the same fundamental processes of interaction of radiation with matter, so of course you get the same equation appearing in scattering theory. Hence by analogy "dispersion & absorption components" for the real & imaginary parts F' & F" of the scattering, and "dispersive difference" for differences delta-F' between different wavelengths.
AFAIK Wayne Hendrickson, who was of course the founder of the MAD technique, always referred to it as "Multi-wavelength Anomalous Diffraction" precisely to avoid this ambiguity of meaning, though I don't know whether it was he who actually coined the acronym MAD. As for whether terminology is important, I believe it was Voltaire who said "If you wish to converse with me, define your terms". -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller > Sent: 22 July 2009 18:03 > To: DebajyotiDutta; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] SAD questions > > I had thought that "dispersion" might be an allusion to > "dispersive differences" which occur between corresponding > amplitudes collected at different wavelengths due to > differences in anomalous scattering. I had explained to > myself, albeit imperfectly, the apparent terminological > inconsistency between the acronyms "MAD" and "SIRAS" by > assuming that since the latter had no dispersive differences, > therefore "SIRAD" would not be appropriate. But then again, > ahem, "SAD?" > > More consistent might be: > > MAD/SAD ==> MIRAD/SIRAD > > MAS/SAS ==> MIRAS/SIRAS > > I think the real explanation is that the acronyms are > inconsistent due to history and personal preferences (based > on ?). Anyway, not an important battle, I don't think. > > Jacob > > PS: Is there a difference in terminology between phasing > using SIR plus MAD versus SIR plus SAD? Are both called "SIRAS?" > > > ******************************************* > 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 > ******************************************* > > > ----- Original Message ----- > From: DebajyotiDutta <mailto:debajyoti_dutt...@rediffmail.com> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Wednesday, July 22, 2009 11:01 AM > Subject: Re: [ccp4bb] SAD questions > > > Dear Sir, > > Thank you all who have replied. It is very nice to have > such a wonderful explanation of Anomalous dispersion and > Anomalous scattering. > > I am sorry to say that SHELXD give me the coordinates > with occ >1. It is not. Actually I am aimed to incorporate > the phases from MR. During this process an iodine data has > been collected. I initially find the substructure with SHELXD > and refined it with SHELXE. Than incorporate the coordiantes > in PHASER EP where I also incorporate the MR structure also. > This give out a pdb file with another atom set where some of > occupancies greater than 1. > > I was just wondering that how the occupancy may get the > value > 1 if it is actually. > > Sincerely > Debajyoti Dutta > > > On Wed, 22 Jul 2009 20:10:06 +0530 wrote > > > >Ian Tickle has just written a definitive answer to your first > >question, so I will just comment on questions 2 and 3. > > > >SHELXD divides the occupancies by the occupancy of the > first atom in > >the peaklist, so they should not be greater than 1.0. > I was not able > >to find an example of an occupancy greater than 1.0 in > a PDB file > >from SHELXD. Assuming that you are using the current version > >of SHELXD (2006/3) I would appreciate receiving more > details. If you > >are using SHELXE for phasing only the RELATIVE > occupancies are used > >anyway. > > > >Some useful statistics are printed out by SHELXC when > it prepares > >the files for SHELXD and SHELXE. If you would like to > display these > >nicely in graphical form you can use Thomas > Schneider's hkl2map GUI > >to call SHELXC/D/E (strongly recommended anyway). > > > >George > > > >Prof. George M. Sheldrick FRS > >Dept. Structural Chemistry, > >University of Goettingen, > >Tammannstr. 4, > >D37077 Goettingen, Germany > >Tel. +49-551-39-3021 or -3068 > >Fax. +49-551-39-22582 > > > > > >On Wed, 22 Jul 2009, DebajyotiDutta wrote: > > > >> Dear Sir, > >> > >> I have very little knowledge about anomalous > dispersion method. The thing is that I have just started to > deal with a case of SAD. I have consulted several text books > to acquire knowledge about it though I have some queries. > CCP4BB, I think is the best place to place my questions. > >> > >> 1.Is there any difference between Anomalous > Dispersion and Anomalous Scattering? > >> > >> 2.Sometimes I found that while searching for > anomalous scatterer with SHELXD which give the coordinates of > the scatterer in PDB format with occupancy more than 1. Why > anomalous occupancy may be more than 1. > >> > >> 3.I found that there is one plot (FPH FP)/FP Vs > Resolution indicate the isomorphism but how can I get this > plot does SHELX has any option to print it. > >> > >> > >> Thank you all for your time and reply to a beginners > query in advance. > >> > >> Sincerely > >> Debajyoti Dutta > >> > > > <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.redif > fmail.com/signatureline....@middle?> > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. 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