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Re: [ccp4bb] Could I improve an inconsecutive experimental map? |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Could I improve an inconsecutive experimental map? From: Fengyun Ni alpharyun {- at -} GMAIL {- dot -} COM Date: 2009-03-11 Hi, I have tried SHARP, but no positive results could be obtained. Do you have some articles on how to combine the model phase and experimental phases? I could only seen the consecutive density in mir 8 to 6 A resolution map, so I could only locate roughly the position of helix. After that I use this helix to calculate the structure factor in SFALL. In SIGMAA, what's the DAMP coefficient should I use? After combination, do I need to do density modification? Hope for your help! Regards, Alphar 2009/2/21 Charlie Bond > Hi Alphar, > A while ago I had success with a poor MIR map by building in a few > fragments I could identify and then combining phases from this model with > the MIR phases using SIGMAA (CCP4 program) and then calculating new maps. A > couple of cycles of this resulted in phases in which I had confidence and I > was able to build the complete structure. (There's probably a more modern > way to do this now ...) > Cheers, > Charlie > > > Quoting Fengyun Ni > > Thanks, Ezra! >> >> I have a native dataset. >> >> I'll try what you said, Hope it works in my case. >> >> Thanks! >> >> Alphar >> >> 2009/2/21 Ezra Peisach >> >> Personally, I would try to build into what you see and then do >>> >> phase > >> recombination. I had a SeMet crystal in which I could only see >>> >> part of a > >> sheet and helix after DM... Things were not connected - until I >>> >> improved > >> the phases with my model. Also - do you have a native dataset? >>> >> You do not > >> mention it. >>> >>> Ezra >>> >>> >>> >>> Fengyun Ni wrote: >>> >>> Hi everyone! >>>> I have a question on my poor MIR map. Four datasets (two AU and >>>> >>> two HG) > >> were used for phasing upto 3 A resolution in my case. I could locate >>>> several >>>> heavy atom sites for each dataset with occupancy finally refined >>>> >>> to about > >> 0.3 to 0.4, and with B value refined to about 50 to 80. I did not >>>> >>> include > >> the anomalous data because once I refine against anomalous data, >>>> >>> the > >> anomalous occupancy was only about 0.02, and even smaller as >>>> >>> 0.004 for some > >> sites. I guess the anomalous data are not good enough, so I did not use >>>> them >>>> right now (Could I do this? Or must I include them somehow?). >>>> The FOM I got is about 0.6, the Cullis-R factors were about 0.6 >>>> >>> for all > >> four data sets, and the phasing power was about 2.5 in each dataset. >>>> After I >>>> did the density modification, the FOM could increas to about 0.8. >>>> My problem is that the protein should form a long helix >>>> >>> structure as > >> indicated by other homology protein, but in the map after density >>>> modification, the densities are not consecutive though the >>>> >>> overall shape > >> seemed to be a long helix. The good thing is that some short >>>> >>> helix-like > >> densities could be observed in the current map, but they are not >>>> >>> connected > >> to each other. >>>> Right now, I am totally lost whether I should believe in the >>>> >>> mir-map I > >> have. Could I improve this map with some other method? Or should >>>> >>> I > >> re-do the >>>> phasing? >>>> BTW, the space group for my crystal is R3 or R32 with a=50, b=50, >>>> >>> c=380, > >> alpha=90, beta=90 and gamma=120. The c-axis is much longer than >>>> >>> a- and > >> b-axis, so the reflection data suffered from the anisotroy >>>> >>> effect. > >> Any suggestion on my phasing problem is welcome. >>>> -- >>>> Alphar Ni >>>> Call me alphar~ >>>> :) >>>> >>>> >>> >>> >> >> -- >> Fengyun Ni >> Call me alphar~ >> :) >> >> > -- > Charlie Bond > Professorial Fellow > University of Western Australia > School of Biomedical, Biomolecular and Chemical Sciences > M310, 35 Stirling Highway > Crawley WA 6009, Australia > > > -- Fengyun Ni Call me alphar~ :) CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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