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 <<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
--
***********************************
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
|
