On 12/03/2013 09:45 AM, Jeff Headd wrote:
Hi Andreas,
We have seen in the past some cases that cause Reduce to go into an infinite loop, which I thought had been corrected, but perhaps your model has found a corner-case that I have not considered. NCS vs. no NCS is not the direct problem, it likely has to do with a particular set of coordinate positions that you are reaching during refinement which causes the hydrogen position determination to end up in either an infinite loop, or just an optimization that isn't tractable in a reasonable amount of time. Hydrogens are added for both NQH flips and for clashscore calculation if your input model does not have them.
To provide an additional datapoint, several of our users have experienced similar hangs with reduce. Tests of one of the jobs reach "Exporting results," and then reduce runs until killed. This is the case even for rigid-body refinement. The hangup occurs under Linux with Phenix 1.8.4-1496 and with Phenix 1.8.3-1479 (subsequently tried for diagnostic purposes). Some users have no such problem running the latest Phenix release; I have not yet determined conclusively what distinguishes between them, but the problem job used for testing involves large molecules with numerous NCS groups at 2.8 Angstroms. If users fall back to Phenix 1.8.2-1309 (our default until recently), the problem is reported to go away, which I have independently confirmed for the test case. Regards, Michael Strickler -- Michael Strickler, Ph.D. Research Specialist Richards Center for Structural Biology Yale University 260 Whitney Ave, 355C JWG PO Box 208114 New Haven, CT 06520-8114