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Re: [ccp4bb] Anomalous map creating |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Anomalous map creating From: Guenter Fritz guenter {- dot -} fritz {- at -} UNI-KONSTANZ {- dot -} DE Date: 2009-11-02 Hi Randy, thanks a lot! That explains everything. best regards, guenter > Hi, > > We should probably clarify the documentation on this point. When you > complete the anomalous substructure in Phaser, it's an iterative > process where LLG maps are computed looking for places where anomalous > scattering should be added (or subtracted). New sites are introduced, > and then the next LLG map shows where further changes would be desired > in the anomalous scatterer model. Because the addition of earlier > sites improves the model and the phases, second and subsequent LLG > maps often lead to the addition of further sites. After 3 or 4 > cycles, however, the process usually converges because there is no > clear indication of further sites. At this point, if all has gone > well, the LLG map indeed should be relatively flat and should show > only some noise, because all the information has been extracted to > improve the anomalous scatterer model. And this is the LLG map you > get at the end of log-likelihood-gradient completion. > > If you want to see the initial LLG map, you have to turn completion > off, and then the map coefficients will show you what Phaser is > interpreting in the first round of completion. In our experience, > this map alone will be clearer than a conventional anomalous > difference Fourier, if you're starting from a protein model. But if > we stopped here, then we would lose the benefit of the iterative > completion process. > > All the best, > > Randy Read > > On 2 Nov 2009, at 09:24, Guenter Fritz wrote: > >> Hi, >> I was looking recently for weak anomalous scatterers, when refined >> model is known. >> I used phaser as described here: >> http://www.phenix-online.org/pipermail/phenixbb/2008-July/001136.html >> >> or running phaser from the ccp4 gui "SAD with molecular replacement >> partial structure" >> >> Works very well, I could identify several ions which had been placed >> as water. >> >> However, when I wanted to look at the anomalous LLG maps, I got a bit >> confused with the description on >> http://www.phenix-online.org/pipermail/phenixbb/2008-July/001136.html. >> Using columns FLLG/PHLLG gave a map looking more like noise. >> >> I got the anom. diff. map using fft or directly in coot (you first >> have to generate DANO from F+ and F- with sftools) using columns >> DANO, PHWT , and not PHLLG !?, can somebody comment on this? >> >> This map looked clearly better than the anom. diff. map generated >> using the phases of the refined model (CAD, FFT). >> Best, >> Guenter >> >> ------------------------------ >> phenix.phaser << eof > SAD_LLG_initial.log >> TITLE initial SAD LLG map >> MODE EP_AUTO >> HKLIN my_peak.mtz >> LLGCOMPLETE CRYSTAL no77 COMPLETE OFF >> LLGCOMPLETE CRYSTAL no77 SCATTERING ANOMALOUS >> PARTIAL PDB ref.pdb IDENT 1.0 >> CRYSTAL no77 DATASET peak LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-) >> SIGF-=SIGF(-) >> COMPOSITION PROTEIN MW 68000 NUMBER 1 >> ROOT SAD_LLG_initial >> eof >> >> ------------------------------------ >> fft HKLIN my_peak_sftools1.mtz MAPOUT my_peak_llg.map < >> TITLE llg anom difference map >> LABIN DANO=DANO SIG1=SIGDANO PHI=PHWT W=FOM >> resolution 50. 2.0 >> EOF >>> Hello everybody! >>> >>> I am faced with a problem of calculating an anomalous map from a Se-Met >>> dataset, and >>> I cannot interpret the error message. >>> >>> So, detailed problem description: >>> >>> I was given a Se-Met dataset of my protein. I scaled it in Scala and >>> made .mtz >>> file, but I do not phases. >>> And I cannot do a MR, but I have a coordinate file. This is my >>> situation >>> >>> So, what I did. >>> I made a copy of .mtz and did a refinement in refmac - to generate >>> phases. >>> During that I lost all anomalous data. >>> After I did CAD procedure - I took from original .mtz anomalous data >>> (F(+), >>> F(-), DANO, IMEAN, I(+), I(-), with sigmas) and from refined mtz - H >>> K L >>> FreeR_flag, F, SIGF, FC, PHIC, FC_ALL, PHIC_ALL, FWT, PHWT, DELFWT, >>> PHDELWT, >>> FOM. >>> And then I did anomalous FFT >>> in the fields I put: >>> PHI - PHIC >>> Weight - FOM >>> DANO - DANO >>> Sigma - SIGDANO >>> >>> I tried with and without excluding of R-free, but result was the same - >>> "FAILED"... And error message was >>> "FFTBIG: No reflexions pass acceptance criteria! Check RESOLUTION, >>> EXCLUDE, missing data." >>> And I cannot find how to fix this. >>> >>> It have also one more warning message - * Missing value set to NaN >>> in input >>> mtz file >>> but as I read it is not a problem - mtz is still readable. >>> >>> I would be glad for any help or advice. >>> Thanks. >>> >>> Sergii >>> >>> P.S. Please, find attached mtz and logs. >> >> >> -- >> *********************************** >> >> Priv.Doz.Dr. Guenter Fritz >> Fachbereich Biologie >> Sektion Naturwissenschaften >> Universitaet Konstanz >> http://www.biologie.uni-konstanz.de/fritz >> >> Universitaetsstrasse 10 >> Postfach M665 >> D-78457 Konstanz >> >> e-mail: guenter.fritz@uni-konstanz.de >> >> Phone Office: +49-(0)7531 88 3205 Phone Lab : +49-(0)7531 88 3733 >> Fax: +49-(0)7531 88 2966 > > ------ > 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: rjr27@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk -- *********************************** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.fritz@uni-konstanz.de Phone Office: +49-(0)7531 88 3205 Phone Lab : +49-(0)7531 88 3733 Fax: +49-(0)7531 88 2966 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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