| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | Advert | | |
Re: [ccp4bb] Could I improve an inconsecutive experimental map? |
||
- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Could I improve an inconsecutive experimental map? From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2009-03-12 I presume you have done density modification after calculating the exptl phases? If you use REFMAC to refine your partial model with the exptl/density modified phase restraints your FWT PHWT fourier coefficients already use the combined phase. I am not sure how to choose a damping factor. If you think the exptl/dm phases are good and have realistic weights I guess there shouldnt be one.. SHARP claims to get the weights more or less right; parrot is meant to do a better job of weighting than DM. Eleanor Fengyun Ni wrote: > 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 >> >> >> >> > > > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
|
| ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd |