On Wednesday 22 July 2009 10:03:19 Jacob Keller wrote:
> 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. 

No. These terms were inherited from another field, as Ian pointed out.

Optical "Dispersion" is the effect that leads to a rainbow when you pass
white light through a prism, and arises because of a change in the optical
index of the medium as a function of the wavelength (energy) of the light.
This dispersion function is normally monotonic.   When materials were found
for which the function was not monotonic, they were considered "anomalous"
and the function itself was an anomalous dispersion function.
 
> PS: Is there a difference in terminology between phasing using SIR plus MAD
> versus SIR plus SAD?  Are both called "SIRAS?" 

To the best of my recollection, the term SIRAS originally referred to the 
use of anomalous differences to "resolve" (i.e. choose between) the ambiguous
pair of phase estimates derived by single isomorphous replacement.
It was popularized by BC Wang
  Wang, B. C. (1984a) Acta Crystalogr., 40A, C12.
  Wang, B. C. (1984b) in Diffraction Methods in Biological Macromolecules
and may have stood for Single Isomorphous Resolved by Anomalous Scattering.

That mathematical approach is not used any more; instead we use the
anomalous and isomorphous differences jointly to derive a single phase
estimate.

	Ethan


> 
>   ----- Original Message ----- 
>   From: DebajyotiDutta 
>   To: [log in to unmask] 
>   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 
>   >> 
>        
> 



-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742