Dear all, I'm refining a structure with 11 molecules in the asymmetric unit. Recently I took out NCS (data are to 2.2A and differences between molecules of interest). Refinement now stalls halfway through with two reduce jobs running at 100% CPU. The current job has been sitting like this for four days. The last entry in the log file are a few XYZ individual lines. Refinement includes XYZ, TLS, individual B, weight optimization. I launched 8 cycles. Phenix hangs after 4_bss. I've observed this twice in a row. Any suggestions to overcome this, short of going back to using NCS? This is with Phenix dev-1538 on RHEL 6.3. Thanks. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
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.
Would you be willing to send me your files (off list) for debugging
purposes? If I can recreate the behavior here, I'll be able to figure out
exactly where Reduce is getting hung up.
Thanks,
Jeff
On Tue, Dec 3, 2013 at 8:11 AM, Andreas Förster
Dear all,
I'm refining a structure with 11 molecules in the asymmetric unit.
Recently I took out NCS (data are to 2.2A and differences between molecules of interest). Refinement now stalls halfway through with two reduce jobs running at 100% CPU. The current job has been sitting like this for four days. The last entry in the log file are a few XYZ individual lines.
Refinement includes XYZ, TLS, individual B, weight optimization. I launched 8 cycles. Phenix hangs after 4_bss. I've observed this twice in a row.
Any suggestions to overcome this, short of going back to using NCS?
This is with Phenix dev-1538 on RHEL 6.3.
Thanks.
Andreas
-- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
curiously, I observed the same thing yesterday in a refinement of a large a.u. (9 chains of just under 400 aa each), I only had 11 hours patience before cancelling the job. In my case I am using MacOSX Snow Leopard and Phenix 1.8.4-1496, which was when I installed it recently the latest "stable" version. I am rerunning it with more processors to see what happens and it has at least passed that same stage. Also, the same job but without including secondary structure restraints finished correctly. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Dec 2013, at 14:11, Andreas Förster wrote:
Dear all,
I'm refining a structure with 11 molecules in the asymmetric unit.
Recently I took out NCS (data are to 2.2A and differences between molecules of interest). Refinement now stalls halfway through with two reduce jobs running at 100% CPU. The current job has been sitting like this for four days. The last entry in the log file are a few XYZ individual lines.
Refinement includes XYZ, TLS, individual B, weight optimization. I launched 8 cycles. Phenix hangs after 4_bss. I've observed this twice in a row.
Any suggestions to overcome this, short of going back to using NCS?
This is with Phenix dev-1538 on RHEL 6.3.
Thanks.
Andreas
-- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Andreas Förster -
Jeff Headd -
Mark J van Raaij -
Michael Strickler