Hi, Since you posted the whole data set to the BB (a link to a file-sharing website might have been better), I took a look at it with other tools. Perhaps I’m running a later version of phenix.xtriage, as in my hands a moderate amount of anisotropy is found. Similarly, Phaser finds a moderate amount of anisotropy.
I suspect what you have uncovered here is a bug in the version of ctruncate that you were using, leading to the negative eigenvalues. Your data set is relatively incomplete, and the incompleteness itself is highly anisotropic, which can be seen for instance with hklview in CCP4. However, I’m not getting the same results, using version 1.15.10 of ctruncate from CCP4-6.4 on a Mac (I haven’t updated yet to 6.5). Which version of ctruncate and which operating system were you using? Best wishes, Randy Read ----- 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 On 13 Jan 2015, at 00:34, Xiao Lei <xiaolei...@gmail.com> wrote: > Hi Eleanor, > > Thank you for the advice. The .sca file is here. The data may not be useful > as you said, but the anisotropic analysis for this data is confusing. From > the phenix xtriage output, it seems the data has no anisotropic issue (I may > interpret wrong the log file, I attach part of the xtriage log file here). > But from CCP4, I know the data has anisotropic problem (Negative > Eigenvalues). > > Below is part of log file from Phenix. > > ---------------- Anisotropy analyses ---------------- > > Anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) : 3.233e-01 > Anisotropic ratio p-value : 0.000e+00 > > The p-value is a measure of the severity of anisotropy as observed in > the PDB. > The p-value of 0.000e+00 indicates that roughly 100.0 % of datasets > available in the PDB have > an anisotropy equal to or worse than this dataset. > > Xiao > > On Sun, Jan 11, 2015 at 7:51 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > Well - I really need to see the output.sca file with the reflection list to > test the problem properly, but this log file does show your reflections at > the highest resolution are very weak, and maybe not useful. Try cutting the > resolute a bit and see what happens. > Eleanor > > On 11 January 2015 at 00:08, Xiao Lei <xiaolei...@gmail.com> wrote: > Hi Eleanor, > > Thanks for the input, I attach the scale log file here. > > On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > Certainly a negative eigen value is bad - can you attach the data? There may > be some obvious problem.. > Eleanor > > On 10 January 2015 at 04:42, Xiao Lei <xiaolei...@gmail.com> wrote: > Dear All, > > I tried to convert my x-ray diffraction sca data from HKL200 (.sca file) to > mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should I > supposed to do next to correct the problem, any suggestions are appreciated. > I pasted the message from part of log file below: > > > ANISOTROPY ANALYSIS (using intensities): > > > Eigenvalues: -0.5668 0.1479 0.3584 > > Eigenvalue ratios: -1.5815 0.4128 1.0000 > > ctruncate: Anisotropy correction failed - negative eigenvalue. > > Times: User: 0.4s System: 0.0s Elapsed: 0:00 > > *************************************************************************** > > * Information from CCP4Interface script > > *************************************************************************** > > The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate -hklin > "/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp" -hklout > "/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp" -colin > "/*/*/\[IMEAN,SIGIMEAN\]" -colout P1_12 > > has failed with error message > > ctruncate: Anisotropy correction failed - negative eigenvalue. > > ObjectCache: Leaked 0005 refs to > > *************************************************************************** > > > > #CCP4I TERMINATION STATUS 0 " ctruncate: Anisotropy correction failed - > negative eigenvalue. ObjectCache: Leaked 0005 refs to > > " > > #CCP4I TERMINATION TIME 09 Jan 2015 19:55:50 > > #CCP4I MESSAGE Task failed > > > > > > > <P1_12_P1_rej2.6_output.sca>
