[ccp4bb] Phaser error: Reflections are not a unique set by symmetry
Hi ccp4ers, I am currently trying to process a crystallographic data set from a 20kDa dumbbell shaped protein which was collected on a Bruker Proteum series detector. The crystal was badly twinned so the Bruker program CELL_NOW was used to find twin domains within the data. While it seperated the data into ~25 different domains it was found that ~ half of the reflections belonged to one domain. Visual inspection of the spot prediction for the unit cell in this major domain looked good; most of the predicted spots were present with good alignment even though there was quite a few additional spots from other domains. This major domain was indexed and integrated on its own (without the other domains) using the Proteum 2/Saint software that supports the detector. Unscaled, unmerged reflections were then imported into ccp4 using combat and run through scala and ctruncate to scale. merge and convert to SFs. However when I then fed this output into phaser the program failed at the anisotropy correction module stating, FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry Does this suggest I still have issues with twinning/scaling or is it that Ive got the space group wrong (currently thought to be P212121)? What specifically are the likely causes of this error message in Phaser? Thanks in advance for your advice, John Chipperfield
Re: [ccp4bb] Phaser error: Reflections are not a unique set by symmetry
Two suggestions for the data processing: 1) The more recent versions of Pointless (since 1.4.3, and better since 1.4.9) can read SAINT output and may do a better job than combat 2) You could scale the data in the Bruker programs and import merged data to CCP4 Phil On 15 Jun 2010, at 10:19, John Chipperfield wrote: Hi ccp4ers, I am currently trying to process a crystallographic data set from a 20kDa dumbbell shaped protein which was collected on a Bruker Proteum series detector. The crystal was badly twinned so the Bruker program CELL_NOW was used to find twin domains within the data. While it seperated the data into ~25 different domains it was found that ~ half of the reflections belonged to one domain. Visual inspection of the spot prediction for the unit cell in this major domain looked good; most of the predicted spots were present with good alignment even though there was quite a few additional spots from other domains. This major domain was indexed and integrated on its own (without the other domains) using the Proteum 2/Saint software that supports the detector. Unscaled, unmerged reflections were then imported into ccp4 using combat and run through scala and ctruncate to scale. merge and convert to SFs. However when I then fed this output into phaser the program failed at the anisotropy correction module stating, FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry Does this suggest I still have issues with twinning/scaling or is it that Ive got the space group wrong (currently thought to be P212121)? What specifically are the likely causes of this error message in Phaser? Thanks in advance for your advice, John Chipperfield
Re: [ccp4bb] Phaser error
This turns out to be a failure in the (rarely exercised) code to read in the substructure with a .ha file. We almost always use PDB files from Hyss or SHELXD to enter the initial substructure, then Phaser .sol files if there's a reason to carry on refinement. The bug has now been fixed for the version of Phaser that will appear in CCP4 6.1 and the next release of Phenix. In the meantime, you can work around it by using PDB files and not HA files for the substructure. Many thanks to Sarah for reporting the bug! Randy Read On Jun 9 2008, Wisecarver, Sarah N wrote: I am attempting to solve a 28kDa protein structure by sulfur anomalous scattering in Phaser for EP (2.1.2). Phaser crashes immediately and I get the following error in the log file. Thanks in advance for your input. Sarah Wisecarver EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.01 secs (0.01 secs) Finished: Fri Jun 6 15:15:02 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: phaser has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 06 Jun 2008 15:15:02 #CCP4I MESSAGE Task failed
[ccp4bb] Phaser error
I am attempting to solve a 28kDa protein structure by sulfur anomalous scattering in Phaser for EP (2.1.2). Phaser crashes immediately and I get the following error in the log file. Thanks in advance for your input. Sarah Wisecarver EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.01 secs (0.01 secs) Finished: Fri Jun 6 15:15:02 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: phaser has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 06 Jun 2008 15:15:02 #CCP4I MESSAGE Task failed
Re: [ccp4bb] Phaser error
Could you add information about - operating system - computer platform - version of phaser - how ccp4 was installed (binary or from source)? Maybe you are trying to run a Mac binary on the wrong platform? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 9 Jun 2008, Wisecarver, Sarah N wrote: I am attempting to solve a 28kDa protein structure by sulfur anomalous scattering in Phaser for EP (2.1.2). Phaser crashes immediately and I get the following error in the log file. Thanks in advance for your input. Sarah Wisecarver EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.01 secs (0.01 secs) Finished: Fri Jun 6 15:15:02 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: phaser has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 06 Jun 2008 15:15:02 #CCP4I MESSAGE Task failed
