[phenixbb] phenix-1.7.2-x refine error

Nathaniel Echols nechols at lbl.gov
Thu Nov 24 09:53:45 PST 2011

On Thu, Nov 24, 2011 at 9:46 AM, Christoph Parthier
<cparthier at googlemail.com> wrote:
> Using the current phenix version, refinements of a 'certain structure'
> always stop with the error message quoted below, while the refinement of
> other 'similar structures' work flawlessly.
> In the error case the three scheduled macrocycles of refinement seem to
> finish (the refined PDB is there) but at there seems to be problem in
> finishing the job - the output MTZ file has zero byte length and the last
> line in refine.log is:
> ...
> This occurs with several 1.7.2-x versions of phenix, I'm not sure about
> 1.7.1-x. Interestingly, the 'problem structure' can be refined without
> problems using the same input files in phenix-1.7-650.
> Any idea whether this is due to an installation problem or a bug?

Probably neither - you're just running out of memory.  My guess is
something in the map-related calculations changed between 1.7.1 and
1.7.2 that made it less memory-efficient (I've seen the same error a
lot recently).  You're using a 32-bit OS, so the maximum amount of
memory that Phenix can use is limited to 2GB - if your hardware
supports a 64-bit kernel, that may solve the problem.  I'd also
recommend trying the latest nightly build, which should consume less
memory creating maps, although I'm not sure if will help with this
specific case.


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