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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 > > > > > > >