So whence the term "dispersive differences" between wavelengths? I believe
that is the proper term, no? Was it just a historical accident based on poor
understanding of the original meaning? I think that is the term used by some
pretty big names in crystallography.
and may have stood for Single Isomorphous Resolved by Anomalous
Scattering.
And what happened with MIRAS? Acronymic gene duplication?
Also, what about my question as to the existence of a terminological
difference between SIR+MAD versus SIR+SAD? I suppose it is always obvious
from the context/publication what was done for phasing?
JPK
*******************************************
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]
*******************************************
----- Original Message -----
From: "Ethan Merritt" <[email protected]>
To: "Jacob Keller" <[email protected]>
Cc: <[email protected]>
Sent: Wednesday, July 22, 2009 12:44 PM
Subject: Re: [ccp4bb] SAD questions
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: [email protected]
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
