[ccp4bb] refmac5 problem
Dear all, What's the difference between no prior phase information, phase and FOM, Hendrickson-Lattman coefficients, and SAD data directly in the refmac5 GUI of CCP4i? I have a SAD dataset and solve the phase by phenix.autosol. Now I want to refine the structure by refmac5, which kind of input above I should choose? Another question is in the Refinement Parameters of refmac5. What's the meaning of Use experimental sigmas to weight Xray terms? If I use molecular replacement to solve the structure, shall I uncheck this item? Thanks very much for your help. Best wishes, Q. Cai
Re: [ccp4bb] refmac5 problem
Dear Cai On 5 Nov 2012, at 09:46, Qixu Cai wrote: Dear all, What's the difference between no prior phase information, phase and FOM, Hendrickson-Lattman coefficients, and SAD data directly in the refmac5 GUI of CCP4i? I would use SAD data directly if you have SAD data set. It just means that the program uses observed F+ and F- directly in refinement. This part of the program has been developed by Leiden group so you can direct your questions to them: Navraj S. Pannu r...@chem.leidenuniv.nl Pavol Skubak p.sku...@chem.leidenuniv.nl I am sure they will help you to get started. I have a SAD dataset and solve the phase by phenix.autosol. Now I want to refine the structure by refmac5, which kind of input above I should choose? Another question is in the Refinement Parameters of refmac5. What's the meaning of Use experimental sigmas to weight Xray terms? If I use molecular replacement to solve the structure, shall I uncheck this item? No. It is related with sigmas of observations and it is desirable to use them. Although there are some question marks how sigmas are estimated, they seemed to be better than nothing. regards Garib Thanks very much for your help. Best wishes, Q. Cai Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] refmac5 problem
I don't know what exactly the phenix.autosol output is. If you are satisfied with the solution and have a mtz file containing F sigF HLA etc, then use Hendrickson Lattmann coefficients. If there is only Phase/Fom then use that. I am not sure how you would fare with SAD data directly.. But beware - do the HLs etc combine phases from the existing model and the anomalous signal - if so they may be biased towards the existing model, and make it harder to correct Eleanor On 5 Nov 2012, at 09:46, Qixu Cai wrote: Dear all, What's the difference between no prior phase information, phase and FOM, Hendrickson-Lattman coefficients, and SAD data directly in the refmac5 GUI of CCP4i? I have a SAD dataset and solve the phase by phenix.autosol. Now I want to refine the structure by refmac5, which kind of input above I should choose? Another question is in the Refinement Parameters of refmac5. What's the meaning of Use experimental sigmas to weight Xray terms? If I use molecular replacement to solve the structure, shall I uncheck this item? Thanks very much for your help. Best wishes, Q. Cai
Re: [ccp4bb] refmac5 problem
I am not sure how you would fare with SAD data directly.. If you would like a comparison, check out the refmac paper. http://journals.iucr.org/d/issues/2011/04/00/ba5152/index.html See Figure 1 - this shows model building with ARP/wARP on over 100 data sets using the different Refmac functions that you asked about. The MLHL function is using phase and fom or Hendrickson-Lattman coefficients The Rice function is no prior phase information and the SAD function is using SAD data directly. The figure shows fraction of the model built automatically. If you see lot of red squares on the top left of the diagonal (which you do), this just means the SAD function outperforms the 'Rice' function and you see more Red squares then Blue circles, so SAD performs better than MLHL. You can get more information on individual functions from references cited in the Refmac paper. The top right shows data sets between 80-100% built by all functions: thus, if your model/map is good enough, any function can build it. For SAD data sets that we have collected here, we always use the SAD function even at the end of the refinement and found (unsurprisingly) a lower difference between R-free and R then other functions. As Garib mentioned, Pavol Skubak and/or I are happy to answer any questions. Best wishes, Raj But beware - do the HLs etc combine phases from the existing model and the anomalous signal - if so they may be biased towards the existing model, and make it harder to correct Eleanor On 5 Nov 2012, at 09:46, Qixu Cai wrote: Dear all, What's the difference between no prior phase information, phase and FOM, Hendrickson-Lattman coefficients, and SAD data directly in the refmac5 GUI of CCP4i? I have a SAD dataset and solve the phase by phenix.autosol. Now I want to refine the structure by refmac5, which kind of input above I should choose? Another question is in the Refinement Parameters of refmac5. What's the meaning of Use experimental sigmas to weight Xray terms? If I use molecular replacement to solve the structure, shall I uncheck this item? Thanks very much for your help. Best wishes, Q. Cai
