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: guenter.fr...@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: rj...@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.fr...@uni-konstanz.de
Phone Office: +49-(0)7531 88 3205
Phone Lab : +49-(0)7531 88 3733
Fax: +49-(0)7531 88 2966
