Dear Lu Zuokun
Sorry, I made a 'typo' - the outliers are marked with negative standard
uncertainty. I doesn't look like from the output that there are any in the
mtz-file.
As Eleanor said, the refmac log is probably more informative.
Best,
Tim
On Monday, September 21, 2015 03:37:11 PM Eleanor Dodson wrote:
> Well - you dont need to (indeed shouldnt) discard negative intensities.. -
> F estimates are corrected to reflect statistical distribution of weak
> intensities..
>
> But the aimless log looks sensible, except that you seem to have integrated
> in P21 although the SG is C2 hence the long list of systematic absences .
>
> Do you have a refmac log? You do have the Spacegroup as C2 in your input
> coordinates do you?
>
> Eleanor
>
> On 21 September 2015 at 15:18, luzuok <[log in to unmask]> wrote:
> > I'm using symmetry scale, merge( aimless) in ccp4i. This program use
> > pointless aimless and ctruncate in tandem. (see file attached).
> > How can I discard the negative intensities?
> > Here is the mtz summery in viewHKL
> >
> > Dataset Group Label Type Min Max Number
> >
> > missing % complete Mean Mean abs Resolution low
> > Resolution high 1 0 0 H H -41 38 0
> > 100.0 -5.47 15.70 84.20 2.31
> > 2 0 0 K H 0 36 0 100.0 13.33
> > 13.33 84.20 2.31
> > 3 0 0 L H 0 39 0 100.0 14.75
> > 14.75 84.20 2.31
> > 4 1 1 F_XDSdataset F 20 3519 66 99.8
> >
> > 363.55 363.55 44.82 2.31
> >
> > 5 1 1 SIGF_XDSdataset Q 3.98 67.18 66
> > 99.8 15.34 15.34 44.82 2.31
> > 6 1 1 DANO_XDSdataset D -128.93 130.92 66
> >
> > 99.8 0.07 18.72 44.82 2.31
> >
> > 7 1 1 SIGDANO_XDSdataset Q 0.00 76.98 66
> > 99.8 27.35 27.35 44.82 2.31
> > 8 1 2 F_XDSdataset(+) G 19.67 3519.38 124
> >
> > 99.6 364.12 364.12 44.82 2.31
> >
> > 9 1 2 SIGF_XDSdataset(+) L 5.70 67.18 124
> >
> > 99.6 20.25 20.25 44.82 2.31
> >
> > 10 1 2 F_XDSdataset(-) G 19.67 3519.38 128
> >
> > 99.6 364.25 364.25 44.82 2.31
> >
> > 11 1 2 SIGF_XDSdataset(-) L 5.22 67.18 128
> >
> > 99.6 19.99 19.99 44.82 2.31
> >
> > 12 1 3 ISYM_XDSdataset Y 0 2 66 99.8
> >
> > 0.01 0.01 44.82 2.31
> >
> > 13 1 4 IMEAN_XDSdataset J -14.15 7650.74 66
> >
> > 99.8 153.61 153.83 44.82 2.31
> >
> > 14 1 4 SIGIMEAN_XDSdataset Q 0.43 138.29 66
> >
> > 99.8 5.17 5.17 44.82 2.31
> >
> > 15 1 5 I+XDSdataset(+) K -16.11 7650.74 66
> >
> > 99.8 153.46 153.83 44.82 2.31
> >
> > 16 1 5 SIGI_XDSdataset(+) M 0.00 138.29 66
> >
> > 99.8 7.24 7.24 44.82 2.31
> >
> > 17 1 5 I_XDSdataset(-) K -16.79 7650.74 66
> >
> > 99.8 153.64 153.99 44.82 2.31
> >
> > 18 1 5 SIGI_XDSdataset(-) M 0.00 138.29 66
> >
> > 99.8 7.13 7.13 44.82 2.31
> >
> > 19 2 6 R-free-flags I 0 19 0 100.0
> > 9.51 9.51 84.20 2.31
> >
> >
> >
> > --
> > 卢作焜
> > 南开大学新生物站A202
> >
> > Lu Zuokun, Ph.D. Candidate
> > College of Life Science, Nankai University
> >
> > At 2015-09-21 21:56:59, "Tim Gruene" <[log in to unmask]> wrote:
> > >Dear Lu zuokun,
> > >
> > >how exactly did you convert the file? I would use
> > >pointless -> aimless -> truncate
> > >to end up with a file that contains amplitudes. You can also use XDSCONV.
> > >
> > >The XDS output file contains outliers. They are flagged by a negative
> > >intensity. Some conversion paths may to treat these outliers correctly
> > >and
> > >make refmac produce an error.
> > >
> > >Best,
> > >Tim
> > >
> > >On Monday, September 21, 2015 09:27:05 PM luzuok wrote:
> > >> Hi,
> > >>
> > >> mtz file was converted from XDS_ASCII.HKL using aimless. When
> > >> running
> > >>
> > >> refmac5, it came up with this error message:
> > >>
> > >> Program received signal 8 (SIGFPE): Floating-point exception.
> > >>
> > >>
> > >>
> > >>
> > >> I can see some "?" in the mtz file column.
> > >>
> > >> Any helps or suggestion would be greatly appreciated!
> > >>
> > >> There seems similar discussion in ccp4bb before, but I cannot google
> > >> it.
> > >>
> > >> Best wishes!
> > >>
> > >> Lu zuokun
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> --
> > >>
> > >> 卢作焜
> > >> 南开大学新生物站A202
> > >>
> > >>
> > >> Lu Zuokun, Ph.D. Candidate
> > >> College of Life Science, Nankai University, China
> > >
> > >--
> > >--
> > >Paul Scherrer Institut
> > >Dr. Tim Gruene
> > >- persoenlich -
> > >OFLC/107
> > >CH-5232 Villigen PSI
> > >phone: +41 (0)56 310 5297
> > >
> > >GPG Key ID = A46BEE1A
--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/107
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
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