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: [log in to unmask]
*******************************************
----- Original Message -----
From: "Ethan Merritt" <[log in to unmask]>
To: "Jacob Keller" <[log in to unmask]>
Cc: <[log in to unmask]>
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: [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
>
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