Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
Hi Vaheh, Thank you for point out this. You are right, the crystal is a plate and somehow at certain angles the frames even failed index, I see a lot of rejection spots when integration. From all the suggestions I got so far, I think I have to grow better crystals and try better collecting data strategies next time. Xiao On Tue, Jan 13, 2015 at 6:35 AM, Oganesyan, Vaheh wrote: > I might be completely wrong here but doesn’t it bother that the number > of rejected reflections shown in log file is ~83000? It shows, at least to > me, that either indexing step is far from being correct or crystal is not > really good enough due to defects. > > > > > > > > *Vaheh Oganesyan* > > *www.medimmune.com <http://www.medimmune.com>* > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao > Lei > *Sent:* Saturday, January 10, 2015 7:08 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction > failed > > > > Hi Eleanor, > > > > Thanks for the input, I attach the scale log file here. > > > > On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson > 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 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. > > 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 > > > > > > > > > To the extent this electronic communication or any of its attachments > contain information that is not in the public domain, such information is > considered by MedImmune to be confidential and proprietary. This > communication is expected to be read and/or used only by the individual(s) > for whom it is intended. If you have received this electronic communication > in error, please reply to the sender advising of the error in transmission > and delete the original message and any accompanying documents from your > system immediately, without copying, reviewing or otherwise using them for > any purpose. Thank you for your cooperation. To the extent this electronic > communication or any of its attachments contain information that is not in > the public domain, such information is considered by MedImmune to be > confidential and proprietary. This communication is expected to be read > and/or used only by the individual(s) for whom it is intended. If you have > received this electronic communication in error, please reply to the sender > advising of the error in transmission and delete the original message and > any accompanying documents from your system immediately, without copying, > reviewing or otherwise using them for any purpose. Thank you for your > cooperation. >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
Hi Evans, Thank you very much for the suggestions! I'll post my data on an online file sharing system from now on. Xiao On Tue, Jan 13, 2015 at 5:21 AM, Phil Evans wrote: > It is hard to tell without having the unmerged data (don't post that to > the BB), but running the data through Pointless, Aimless ctruncate (though > I had to fix Aimless) suggests > > 1. the data are not very good > 2. the space group may be C2 > 3. it may be twinned (or just some spot overlap with the long 288A c axis) > > Phil > > On 13 Jan 2015, at 00:34, Xiao Lei 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 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 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. > > > > 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 > > > > > > > > > > > > > > >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
Hi Randy, Thank you very much for the advice. I use CCP4 version 6.4.0 on my Mac OS X 10.10.1, after my updating my Mac OS X to 10.10.1 three weeks ago, I did have a issue to open CCP4, I have to re-install X-Quartz and after that I can open CCP4 well. I haven't updated CCP4 to 6.5, maybe I should update to 6.5 because of somehow I may have a bug on my CCP4 as you said. Xiao On Tue, Jan 13, 2015 at 1:04 AM, Randy Read wrote: > 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 ResearchTel: +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 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 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 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. > > > > 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 > > > > > > > > > > > > > > > >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
I might be completely wrong here but doesn’t it bother that the number of rejected reflections shown in log file is ~83000? It shows, at least to me, that either indexing step is far from being correct or crystal is not really good enough due to defects. Vaheh Oganesyan www.medimmune.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei Sent: Saturday, January 10, 2015 7:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed Hi Eleanor, Thanks for the input, I attach the scale log file here. On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson mailto: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 mailto: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. 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 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
It is hard to tell without having the unmerged data (don't post that to the BB), but running the data through Pointless, Aimless ctruncate (though I had to fix Aimless) suggests 1. the data are not very good 2. the space group may be C2 3. it may be twinned (or just some spot overlap with the long 288A c axis) Phil On 13 Jan 2015, at 00:34, Xiao Lei 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 > 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 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 > 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 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. > > 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 > > > > > > >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
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 ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-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 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 > 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 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 > 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 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. > > 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 > > > > > > >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
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 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 > 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 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. >>> >>> 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 >>> >>> >>> >>> >> >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
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 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. > > 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 > > > >
[ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
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. 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
