Hi Alexandra, You will have to run the last steps in data processing over and obtain anomalous data in order to calculate that anomalous difference map. Once you have that data you can also refine the occupancy of your Mo atom, however at 0.97 A the anomalous scattering from Mo is not strong (f" is 1.2 electrons). All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Alexandra Marques [[email protected]] Sent: Wednesday, June 17, 2015 7:04 AM To: [email protected] Subject: [phenixbb] anomalous difference map calculation Hi, I am in the last refinement steps of a MR model and I want to calculate an anomalous difference map essentially to confirm the presence of a sulfite molecule and to locate vanadium (present in soaking solution). I read that it is necessary to have a mtz file with anomalous data (i.e. F+,F- or I+,I-). However, my data was collected at “normal” wavelenght (0.97) and it was processed with XDS considering Friedls law= true and my mtz file contain the following columns: H K L FP SIGFP. So, can I still calculate a anomalous difference map based on my data? Since I also have a Mo atom in the active site can I try to refine its occupancy by using the option “anomalous groups” in the refinement strategy? Thank you very much, Alexandra

Dear Alexandra, I would like to correct the two previous replies: there is no need to reprocess your data. XDS_ASCII.HKL will contain the anomalous information. The keyword 'FRIEDEL'S_LAW' affects the scaling, but not the output format. Actually some people recommend to always process with FRIEDEL'S_LAW=TRUE whether or not you want to extract the anomalous signal, because to get higher multiplicity for scaling (There are caveats if very strong Friedel/Bijvoet differences are present, but these are rare, I believe). You only need to rerun the conversion program and tell it to keep the Bijvoet pairs separate. The fastest way to create the anomalous difference map is to use shelxc for a SAD experiment. shelxc reads the XDS_ASCII.HKL directly and will also treat it correctly. This creates an _fa.hkl file. When you provide this and your pdb-file to the program anode (also available from the SHELX server), it create the anomalous map (ending .pha) that you can read into Coot. When you are familiar with shelx c/d/e and anode, it would take you maybe 1-2 min to create the map. If you are not familiar with the programs, maybe a few minutes more. Take a look at pages 25-27 in http://shelx.uni-ac.gwdg.de/~tg/teaching/anl-ccp4/pdfs/tgruene_chicago2014_s... for a first guide. Best, Tim On 06/17/2015 03:04 PM, Alexandra Marques wrote:

Hi,

I am in the last refinement steps of a MR model and I want to calculate an anomalous difference map essentially to confirm the presence of a sulfite molecule and to locate vanadium (present in soaking solution). I read that it is necessary to have a mtz file with anomalous data (i.e. F+,F- or I+,I-). However, my data was collected at “normal” wavelenght (0.97) and it was processed with XDS considering Friedls law= true and my mtz file contain the following columns: H K L FP SIGFP. So, can I still calculate a anomalous difference map based on my data?

Since I also have a Mo atom in the active site can I try to refine its occupancy by using the option “anomalous groups” in the refinement strategy?

Thank you very much, Alexandra

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