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
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
>>
