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
