to the original poster: please do not attache several MB files...
Tommi
On Oct 27, 2009, at 11:24 AM, Eleanor Dodson wrote:
Well - doing an mtzdump on testXXX.mtz shows most of the DANO are
missing..
and also most of the F_gp5-gp27(+)_nat so the problem is farther
back..
OVERALL FILE STATISTICS for resolution range 0.000 - 0.119
=======================
Col Sort Min Max Num % Mean Mean
Resolution Type Column
num order Missing complete abs. Low
High label
1 ASC 0 41 0 100.00 19.7 19.7 127.21
2.89 H H
2 NONE 0 24 0 100.00 6.9 6.9 127.21
2.89 H K
3 NONE -131 131 0 100.00 1.5 49.7 127.21
2.89 H L
4 NONE 0.0 19.0 5 99.98 9.48 9.48 64.49
2.89 I FreeR_flag
.....
16 NONE 8.5 4494.8 29499 8.34 895.29 895.29 74.82
2.89 G F_gp5-gp27(+)_nat
17 NONE 6.0 162.8 29499 8.34 37.83 37.83 74.82
2.89 L SIGF_gp5-gp27(+)_nat
18 NONE 8.5 4681.4 353 98.90 812.18 812.18 74.82
2.89 G F_gp5-gp27(-)_nat
19 NONE 5.8 162.8 353 98.90 25.89 25.89 74.82
2.89 L SIGF_gp5-gp27(-)_nat
20 BOTH 0.0 0.0 29499 8.34 0.00 0.00 74.82
2.89 D DANO_gp5-gp27_nat
21 BOTH 0.0 0.0 29499 8.34 0.00 0.00 74.82
2.89 Q SIGDANO_gp5-gp27_nat
The cad log file looks OK so you need to go back to the scala step
and see how this happened.Maybe you didnt measure enough equivalent
observations to get a DANO set?
Eleanor
Sergii Buth wrote:
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.
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
