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 <[email protected]> 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:[email protected]] *On Behalf Of *Xiao > Lei > *Sent:* Saturday, January 10, 2015 7:08 PM > *To:* [email protected] > *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 <[email protected]> > 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 <[email protected]> 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 > > > > > > > > > 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. >
