Hi,
If you're using Phaser to refine the anomalous scatterers, then their
occupancies may indeed refine to numbers > 1. If everything were
perfect (data perfectly on absolute scale, f" precisely correct), then
none of the occupancies should refine above one. Phaser attempts to
put the data on absolute scale, which usually works reasonably well,
but will not be perfect, and the f" isn't necessarily precisely
correct, so there will be errors. However, we usually find that the
highest occupancies are close to one. How much greater are the values
you are finding?
Presumably, when you're combining the MR and SAD information, you're
taking care to get the same origin (and hand) for both. One safe
approach is to start the SAD phasing in Phaser from the MR solution,
and Phaser should then find the anomalous scatterer sites itself. You
can then compare the sites with the ones from SHELXD -- the most
convenient tool for this that I know is phenix.emma.
By the way, when you're using SHELXD sites in Phaser, you probably
have to change the atom type in the SHELXD PDB file from S to whatever
your anomalous scatterer really is!
Regards,
Randy Read
On 22 Jul 2009, at 17:01, DebajyotiDutta wrote:
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
>>
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [email protected]
Cambridge CB2 0XY, U.K. www-
structmed.cimr.cam.ac.uk
