Re: [ccp4bb] Anomalous map creating

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: loop modelling?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-11-02

Next message:
Subject: Re: loop modelling?
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-11-02

Subject: Re: Anomalous map creating
From: Guenter Fritz guenter {- dot -} fritz {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2009-11-02

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: loop modelling?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-11-02

Next message:
Subject: Re: loop modelling?
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-11-02