Dear Sir,
Thank you for your reply. The values I am getting for the occupancies are 1.4, 1.6 and 2.1 etc. I kept the both hand same (MR sol and SAD data). I am highly benefited with these discussions. Sincerely debajyoti On Thu, 23 Jul 2009 00:49:57 +0530 wrote >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 > >
