[phenixbb] Does phenix have any utility to do the 2mFo-DFc composite omit map calculations?

Donnie Berkholz dberkholz at gentoo.org
Wed Nov 3 07:21:02 PDT 2010

On 18:12 Tue 02 Nov     , Nathaniel Echols wrote:
> On Tue, Nov 2, 2010 at 6:02 PM,  <zhangh1 at umbc.edu> wrote:
> > I tried a dimer of 4000aa at 3.2A using the following script:
> >
> > phenix.autobuild data=2VZ8.mtz model=${f}.pdb composite_omit_type=simple_omit
> >
> >  It took hours and ended up with nothing (probably due to memory leaking).
> > Is there anyway to make it faster?
> This is what the 'nproc' argument does - you should use as many
> processors as you have available.  If you can distribute it across a
> queuing system, even better.  (The GUI can set this up for you
> semi-automatically if you have Sun Grid Engine, but it's possible on
> the command line too - check the documentation for details.)  

Now that new versions of SGE will no longer be free thanks to Oracle's 
purchase, have you considered adding support for a queueing system that 
is free and open-source, such as Torque?


Donald S. Berkholz, Ph.D.
Research Fellow
James R. Thompson lab, Physiology & Biomedical Engineering
Grazia Isaya lab, Pediatric & Adolescent Medicine
Medical Sciences 2-66
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905
office: 507-538-6924
cell: 612-991-1321
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