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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 <<EOF > 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: [log in to unmask] > > 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: [log in to unmask] Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk