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

Nathaniel Echols nechols at lbl.gov
Tue Nov 2 18:12:33 PDT 2010

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.)  Unlike
the CCP4 OMIT program, it is actually re-refining many partial models
to remove phase bias, so running it on a single processor isn't going
to work very well.


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