[buster-discuss] ME and memory

[jjwarren at duke.edu]

The Shannon Samplig Rate is 384 384 384.  Is that what you're asking for?

Unfortunately, the data is already cut at 3 A.  It only goes to 2.8 or so,
anyway.  Any other thoughts?  Thanks!

Josh


On Mon, 28 Nov 2005, Clemens Vonrhein wrote:

> Hi,
>
> sorry for the late response!
>
> You probably have also high(ish) resolution data? What does the
> sampling rate (in the LIST.html) tell you? The ME calculation can get
> REALLY big.
>
> So you might want to run a ME job at lower resolution (to cut down on
> the sampling rate). If you're after missing loops/domains, even
> 2.5-3.0A data should tell you something.
>
> Cheers
>
> Clemens
>
> On Mon, Nov 21, 2005 at 10:22:53AM -0500, jjwarren at duke.edu wrote:
> > Hi-
> >
> > I have been trying to use buster to refine an incomplete structure and it
> > seems to be working well, but crashes if I try to do maximum entropy
> > refinement.  I get the following error:
> >
> >
> >    Allocated BUFFER of size:  1732.500 Mb.
> >  Not enough memory to allocate BUFAUX of size:  1732.500 Mb.
> >   Program stopped.
> >  closesok message: time spent in tree = 2097.88 (user)  15.54 (sys)
> >             Error - Not enough memory to allocate BUFAUX of size: 1732.500
> > Mb.
> >
> >
> > I get the same error on two different linux machines which have different
> > amounts of memory.  The larger of the two has 2 Gb RAM, so I am assuming
> > that the problem is with memory allocation in the software and not with
> > the computers' physical memory.  Anyone have a fix/work around, or do I
> > need to try to get a custom version of the program(s)?
> >
> > Pertinent Stats:
> > Running Buster 1.0.2 for linux on Fedora Redhat or SuSe Linux 9.0
> > Protein + missing atoms ~ 240 kDa
> > Unit Cell: 260 260 260 90 90 90, with one molecule in the AU.
> >
> > Also, ME works fine with the tutorial data.
> >
> > Thanks in advance for your help,
> >
> > Josh
> >
> >
> > _______________________________________________
> > buster-discuss mailing list
> > buster-discuss at globalphasing.com
> > http://www.globalphasing.com/mailman/listinfo/buster-discuss
> >
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park
> *  Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group      (http://www.globalphasing.com)
> ***************************************************************
>

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