On Mon, Sep 5, 2011 at 9:13 AM, Tanner, John J.
I get the following error at the end of a phenix.refine run. The pdb file is produced, but the mtz file is empty. The resolution is 1.15 A and the cell is
CRYST1 84.808 93.803 132.080 90.00 90.00 90.00 P 21 21 21
The version is
PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.7.1 Release tag: 743 Platform: intel-linux-2.6 redhat-e5.6
I've seen this sort of thread on the bb previously. Is there a fix for this, other than using refmac?
The recommended fix, I'm afraid, is to install a 64-bit OS (and probably more physical memory as well). Alternately, if you turn off output of maps/map coefficients, it will skip the step that is breaking here (you can use phenix.maps to create the maps later). There are probably several places in the code where we handle memory inefficiently, but debugging these issues is a longer-term project since it's a slow process. If you're willing to share the model and data with us (or alert us when it gets published), this might make it easier to isolate problems. A more general recommendation: when encountering a MemoryError crash in phenix.refine, the first thing to check is whether you have rotamer fitting or solvent update enabled - these both require maps, which tend to be fairly large and poorly optimized for memory use. (This isn't what's breaking in your case, however.) thanks, Nat